Yet Milan's defensive frailty was punished when Konstantinos Fortounis scored from the penalty spot in the 81st minute to give his side the win that left them second in Group F on 10 points.
Arsenal qualified for a 17th successive season with a nervy 1-0 win at home to Besiktas and Malmo made it for the first time with a 3-0 win over Salzburg, whose participation ended in the qualifiers for the ninth time in a row.
Pep Guardiola's ManchesterCity will play Romanian side Steaua Bucharest in the Champions League playoff round after the draw was made in Nyon on Friday.
Arsenal teenager Bukayo Saka scored his first goal for the club as they beat 10-man Eintracht Frankfurt 3-0, while Manchester United's 17-year-old Mason Greenwood secured a 1-0 win over FC Astana as the Europa League group stage began on Thursday.
Arsenal suffered a shock Europa League exit to Olympiakos Piraeus on away goals after a 2-1 extra-time home defeat, while Manchester United and Wolverhampton Wanderers cruised into the last 16 with emphatic aggregate wins on Thursday.
As Barca prepare for a trip to Madrid to play Rayo Vallecano on Saturday, they are still reeling from Tuesday's 3-2 Champions League reverse at Paris St Germain, when their defence was badly exposed by the Ligue 1 title holders.
Holders Real Madrid chased away some of their early-season blues when Gareth Bale scored the pick of the goals in a 5-1 rout of FC Basel in their Champions League Group B opener on Tuesday.
Manchester United, Sevilla and Celtic led a parade of clubs with continental pedigree to book the first places in this season's Europa League knockout stage.
Arsenal's young guns continued to shine as they dismantled Standard Liege 4-0 on a hectic night of Europa League action that produced a full house of Spanish victories on Thursday. A summary of the matches.
Tottenham Hotspur exposed the weaknesses in Anzhi Makhachkala's star-shorn squad, winning 2-0 in Moscow to maintain their perfect start in the second round of Europa League group stage matches on Thursday.
Brazilian-born Marcelinho scored on his Bulgaria debut while Cristiano Ronaldo missed a penalty for Portugal as the visitors pulled off a shock 1-0 friendly win over the Euro 2016 finalists on Friday.
Jonathan Soriano scored an incredible goal from near the halfway line to complete a stunning 3-0 win for Salzburg away to once-mighty Ajax Amsterdam in the Europa League round of 32 on Thursday.
Paris St Germain will play Borussia Dortmund and Barcelona were pitted against an unpredictable Napoli, while Chelsea were drawn against Bayern Munich. City, who will be at home in the second leg, have yet to beat the Spanish side with two draws and two defeats in their previous four meetings.
Pep Guardiola will return to the Nou Camp in the Champions League group stage after his new club Manchester City were drawn against his former Barcelona team on Thursday. The two sides were drawn in Group C alongside Borussia Moenchengladbach and former European champions Celtic in one of the toughest of the eight sections. Spanish coach Guardiola, who won the Champions League twice with Barca, faced the Catalans when he was in charge of Bayern Munich two seasons ago and suffered a 5-3 defeat in the semi-finals.
Basle FC lead online mocking of Liverpool.
Barcelona battled back from a goal down and scored twice in the second half to overcome hosts Borussia Moenchengladbach 2-1 in their Champions League Group C match on Wednesday despite the absence of the injured Lionel Messi.
Goals from Jan Vertonghen and Jermain Defoe left Tottenham Hotspur on the cusp of the Europa League knockout stages as four other clubs maintained perfect starts on Thursday.
Cristiano Ronaldo renewed his personal battle with Lionel Messi by scoring his 71st Champions League goal, putting him three behind the Argentine's newly-set record, in Real Madrid's 1-0 win at FC Basel on Wednesday.
Kazakhstan's Astana fought back to beat a youthful Manchester United side 2-1 at home, Arsenal's woes continued as Frankfurt's Daichi Kamada scored twice to secure a 2-1 win.
Borussia Dortmund snatched a late goal at Atalanta to progress with a 1-1 draw, while AC Milan and Atletico Madrid, both with three-goal leads from the away legs, completed the formality of qualifying with 1-0 wins at home on Thursday.
Unai Emery's side were heading for a demoralising defeat, three days after losing meekly to Sheffield United in the Premier League, but substitute Pepe's late intervention kept the Gunners top of Group F with a maximum nine points.
Images from the UEFA Champions League matches played on Wednesday
Real Madrid coach Carlo Ancelotti hailed his "extraordinary" players after they set a Spanish record for consecutive victories of 19 thanks to a 4-0 success at home to Ludogorets.
You would have been hard pressed at the start of the season to find anyone to bet on Liverpool's Brendan Rodgers becoming the first Premier League manager to get the sack, but he is now the bookies' joint favourite.
Arsenal and Chelsea were among seven teams to reach the Europa League knockout stage on Thursday, while last year's runners-up Olympique de Marseille were eliminated at the group phase.
An injury to playmaker James Rodriguez could prompt Real Madrid to dip into the transfer market next month and they are interested in Cruzeiro midfielder Lucas Silva among others, coach Carlo Ancelotti said on Monday.
Arsenal led a list of nine clubs who grabbed a second win in as many games in the Europa League group phase as France striker Olivier Giroud scored his 100th goal for the club in a 4-2 win at BATE Borisov on Thursday.
Holders Real Madrid chased away some of their early-season blues when Gareth Bale scored the pick of the goals in a 5-1 rout of FC Basel in their Champions League Group B opener on Tuesday.
Mario Balotelli will be available for Liverpool's home Premier League match against Aston Villa on Saturday after recovering from illness, manager Brendan Rodgers said.
Having battled to break down one of Europe's meanest defences in the quarter-finals, Real Madrid will have to do it all over again when they face Juventus in their Champions League semi-final.
Liverpool manager Brendan Rodgers took an upbeat view on a dismal night as the five-times European champions were bundled out of the Champions League following a 1-1 draw with FC Basel at Anfield on Tuesday.
Mario Balotelli admits he is struggling to adapt to Liverpool manager Brendan Rodgers' tactics as he seeks to open his Premier League account for his new club.
Lazio won 2-0 at Legia Warsaw on Thursday to qualify for the Europa League knockout stages after a tie marred by violence when Italian fans fought with Polish police on the way to the stadium.
A KrisCommons header gave former European champions Celtic a 1-0 win over Swedish side Elfsborg Boras while Fenerbahce made the most of their Champions League lifeline with a 1-1 draw against Salzburg in the first leg of their third qualifying round tie on Wednesday.
Real Madrid keeper Iker Casillas believes the European champions have a side with the potential to be one of the all-time greats and it will be with likely trepidation that an off-colour Liverpool visit the Bernabeu on Tuesday.
News of all that's transpired on and off the football field
Lionel Messi, Luis Suarez and Neymar combined to devastating effect as Barcelona swatted Celtic aside 7-0 at the Nou Camp to lay down a marker in Champions League Group C on Tuesday.
Holders Real Madrid breezed into the last 16 of the Champions League with two games to spare when a Karim Benzema strike secured a 1-0 win in their Group B match at home to a toothless Liverpool on Tuesday.
Liverpool see Tuesday's Champions League game at holders Real Madrid as a chance to prove their doubters wrong and get their season back on track, said coach Brendan Rodgers and midfielder Jordan Henderson.
Liverpool's 1-0 defeat by Aston Villa on Saturday was more than an early season setback - it raised the question of whether they have the strength in depth to cope with the dual challenge ahead of them this term.