Florian Thauvin headed in Payet's free kick after 15 minutes and Clinton Njie calmly slotted home in the 63rd to put Marseille in the driving seat against the Austrian champions.
Manchester City came from behind to beat Club Brugge 3-1 and secure their place in the Champions League playoffs
Arsene Wenger's team look likely to return to Europe's most prestigious competition next season.
Several records and milestones were set after Real Madrid beat Liverpool 3-1 in the Champions League final on Saturday. With the victory Real became the first team to win three straight titles in the Champions League era.
Runaway Premier League leaders Manchester City will play Borussia Dortmund with the winners to face either Bayern or PSG in the semi-finals.
Atletico Madrid and Athletic Bilbao should serve up a Europa League final to remember on Wednesday and remind the continent that Spain is not just about Real Madrid or Barcelona.
Spain may have an iron grip on Europe's club competitions but the English Premier League is the dominant power when it comes to the number of players competing at Euro 2016. Spain have won the last two European championships and La Liga clubs have claimed Europe's major club trophies, the Champions League and Europa League, for the last three seasons. Yet a quarter of the 552 players going to Euro 2016 play in the English leagues, nearly four times as many as those from La Liga, according to figures from Grosvenor Casinos.
Sevilla's Kevin Gameiro grabbed a late equaliser in a 2-2 draw at Zenit St Petersburg on Thursday to send the Europa League holders into the semi-finals after woeful goalkeeping had threatened to ruin their night.
Ten Hag's contract was set to expire at the end of the 2024-25 season but denying Manchester City a domestic double and qualifying for the Europa League earned him another chance.
Images from Thursday's action in the Premier League.
Alex Ferguson may have been stripped of his Manchester United ambassadorial role last week but his legacy as manager remains a stifling cloud for those following in his footsteps, with Erik ten Hag the latest to be jettisoned after failing to measure up.
Manchester City won an unprecedented fourth straight English top flight title with a 3-1 win over West Ham United.
Porto's Radamel Falcao scored a hat-trick to help the newly-crowned Portuguese champions thrash Spartak Moscow 5-1 as goals flowed and South American players shone in Europa League quarter-final first leg ties on Thursday.
Five-times European champions Liverpool survived a late scare to move into the last 32 of the Europa League with a 1-0 win over Italian side Udinese on Thursday.
Liverpool boss Juergen Klopp has said his team will be 'on fire' for the Champions League final
Manchester United crushed Newcastle United's hopes of a claiming a first domestic trophy for nearly 70 years with a clinical 2-0 victory in the League Cup final at Wembley on Sunday.
Manchester City's Erling Haaland faces Borussia Dortmund and Barcelona's Robert Lewandowski meets Bayern Munich after the Champions League group-stage draw was made on Thursday.
Romanians Astra handed West Ham United their first competitive defeat at the London Stadium as Slaven Bilic's team were beaten in the Europa League playoffs on Thursday.
Tottenham Hotspur trounced a sorry Inter Milan 3-0 in the Europa League on Thursday while last year's European champions Chelsea were humbled 1-0 by Steaua Bucharest after being stung by a Raul Rusescu penalty.
AC Milan grabbed a 1-1 draw at Manchester United in the blockbuster Europa League last-16 first-leg at Old Trafford on Thursday.
The race for Premier League places in next season's Europa League warmed up on Sunday when Aston Villa and Everton fought out a thrilling 3-3 draw and Fulham came from behind to win 3-1 at Manchester City.
Fernando Torres left Chelsea fans wondering if they would ever see the striker who once terrorised defences after another forlorn performance as they limped into the last 16 of the Europa League 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.
Lazio have been fined 40,000 euros for racist behaviour by their fans during the Europa League tie at Tottenham Hotspur last month, UEFA said on Thursday.
Man United out of Europe after 1-0 home loss to Bayern Munich
Liverpool full back Nathaniel Clyne is eager to end Manchester United's Europa League campaign after losing both Premier League matches against their arch rivals for a second successive season. English football's most successful clubs meet for the first time in Europe on Thursday in the first leg of their last-16 clash at Anfield, with Liverpool aiming for revenge after a 1-0 home loss in January and 3-1 defeat at Old Trafford in September. "I think we owe them from the Premier League games, which we probably should have got more out of. But we have time now to put things right and progress through the cup," Clyne told British media.
'So, the Champions League final will be played between two teams who just don't know when they are beaten,' says Suhit K Sen.
Chelsea are in the last chance saloon as far as a trophy goes and Fernando Torres, complete with his 'Mask of Zorro', must continue his recent improvement in swashbuckling style in Thursday's Europa League semi-finals.
Diego Forlan's extra-time effort sent Atletico Madrid into the Europa League final on away goals at the expense of Liverpool after a 2-2 aggregate draw on Thursday. Atletico will meet Fulham in the May 12 final in Hamburg where they will bid to win their first major European trophy since the European Cup Winners' Cup in 1962.
Former UEFA Cup winners Anderlecht reached the Europa League knockout stage with the only perfect record on Thursday and were joined in the last 32 by Athletic Bilbao, Legia Warsaw, PSV Eindhoven and Twente Enschede with two games to spare.
'I think that the only thing that we lacked was to convert the chances. We were good in the high press. After going behind, we generated 20 chances and six or seven were very clear.'
Egemen Korkmaz's second-half header earned Fenerbahce a 1-0 win in the first leg of their Europa League semi-final against Benfica and eased the tears of team mate Cristian on Thursday.
A round-up of Wednesday's action in the UEFA Champions League.
Rodrigo Palacio snatched an 88th minute win for Inter Milan over Partizan Belgrade in the Europa League on Thursday while Lazio were on the wrong end of some late drama in a 1-1 draw at Panathinaikos.
UEFA president Aleksander Ceferin said they were committed to "qualification based on sporting merit".
Liverpool will be without key duo Steven Gerrard and Fernando Torres for Thursday's Europa League playoff second leg away to Trabzonspor.
Marcus Rashford has made more appearances than any other player at the club this season
Real Sociedad will join Atletico Madrid, Real Madrid, and LaLiga champions Barcelona in Europe's elite club competition next season.
Manchester City's Brazilian keeper Ederson won the Golden Glove award.
Fernando Llorente netted a dramatic late winner for Athletic Bilbao to eliminate Sporting and Atletico Madrid comfortably held on to a first-leg lead to oust La Liga rivals Valencia on Thursday and set up an all-Spanish Europa League final.
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