Barcelona and Bayern fought hard but failed to break the shackles until the 77th minute in the match when Messi struck the first and three minutes later struck his 77th Champions League goal to double Barca's advantage.
Real Madrid and Barcelona pulled two points clear in La Liga when Cristiano Ronaldo set a club scoring record in Real's 3-0 stroll against Levante and Neymar hit four as Barca beat Rayo Vallecano 5-2 on Saturday.
Real Madrid closed to within three points of La Liga leaders Barcelona and Atletico Madrid at the halfway stage of the season when a Pepe header secured a laboured 1-0 win at mid-table Espanyol on Sunday.
Celta Vigo thrashed Barcelona 4-1 on Wednesday with Iago Aspas hitting a double.
Cristiano Ronaldo's bullet header helped Real Madrid to a 2-0 victory .
Lionel Messi notched his 250th La Liga goal to move one off the all-time league scoring record as leaders Barcelona won 3-0 against Eibar on Saturday ahead of next weekend's Clasico with Real Madrid.
Barcelona finished three points behind Real Madrid last season but there is concern the gap between Spain's biggest two sides could be far larger this season.
Cristiano Ronaldo struck twice as leaders Real Madrid subdued Eibar 4-0 on Saturday while Lionel Messi set a La Liga record of 253 goals with a hat-trick in second-placed Barcelona's 5-1 rout of Sevilla.
Real Madrid have enviously looked on as Barcelona claimed six La Liga titles in the last eight years, but Zinedine Zidane's side can take a huge step towards a first crown since 2012 with victory over their bitter rivals at the Nou Camp on Saturday.
Manchester City's midfield powerhouse Yaya Toure will leave the club at the end of the season having not been offered a new contract, his agent said on Monday.
Images from the UEFA Champions League matches played on Wednesday.
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.
Real Madrid coach Zinedine Zidane says Frenchman Karim Benzema is "distraught" about being left out of the squad for this year's European Championship, the only major tournament to be played in his home country during his career.
A summary of Wednesday's matches in the UEFA Champions League.
A Gareth Bale header and a Cristiano Ronaldo penalty gave Real Madrid a much-needed 2-0 victory over Eibar in La Liga on Sunday, following their hammering by leaders Barcelona last weekend, and put them six points off the top of the standings.
The Bernabeu faithful have never taken Gareth Bale to their hearts with injury problems and a perceived lack of integration into the side often used as sticks to beat him with.
A round of Saturday's matches in Series A, La Liga and Bundesliga.
Images from the football matches played across Europe on Sunday
Gary Neville's disappointing start as Valencia coach continued when the ambitious Singapore-owned club drew 2-2 at home to lowly Rayo Vallecano in La Liga on Sunday, prompting more rumblings of discontent from the fans.
Barcelona's Neymar struck twice to put the Spanish side in the Champions League final despite a 3-2 loss at Bayern Munich on Tuesday as they progressed 5-3 on aggregate and will face Real Madrid or Juventus next month.
La Liga leaders Real Madrid returned to winning ways after two defeats, making light of playing most of the second half with 10 men to triumph 3-0 at home to mid-table Espanyol on Saturday.
Prolific Cristiano Ronaldo hit a 35th hat-trick for Real Madrid who swept aside Espanyol 6-0 in a ruthless attacking display in La Liga on Sunday.
Barcelona goalkeeper Victor Valdes is likely to be out of action until the end of the year after suffering a calf strain during Spain's surprise defeat by South Africa on Tuesday, the club said in a statement on their website.
Cristiano Ronaldo scored twice as Juventus strolled to a 3-0 home win over bottom side Crotone in the Italian Serie A on Monday, with the victory taking the champions up to third in the standings.
Sacked Real Madrid coach Rafa Benitez says it was "an honour and privilege" to lead the club he has always supported and has sent a "good luck" message to his successor, former France great Zinedine Zidane.
Coach Zinedine Zidane learned the lessons of predecessor Rafael Benitez's disastrous tactics in the last encounter and employed defensive midfielder Casemiro in favour of more attack-minded players, opting instead to sit and wait for Barcelona.
Barcelona and Brazil striker Neymar has launched an attack on his former club Santos and spoken out in support of his father, insisting he had the right to make millions from the player's transfer last year.
Real Madrid lifted the FIFA Club World Cup for a record fourth time on Saturday after thrashing local side Al Ain 4-1 in the final in Abu Dhabi with the help of impressive distance strikes in either half from midfielders Luka Modric and Marcos Llorente.
This time we're ready for Barca, says Man City's Nasri.
Real Madrid have sacked coach Rafa Benitez after less than half a season in charge and promoted their former France great Zinedine Zidane from the B team to replace him, president Florentino Perez said on Monday.
New Valencia coach Gary Neville remains without a La Liga win after his side twice recovered from a goal down to rescue a fortunate 2-2 draw at home to Getafe on Saturday.
Real Madrid fans could be forgiven for wondering whether a new president is needed rather than yet another new coach after Carlo Ancelotti was sacked.
Real Madrid brushed off the absence of Cristiano Ronaldo and Gareth Bale to beat Espanyol 2-0 away and maintain their 100 per cent start to the league season while matching the La Liga record of 16 consecutive victories.
News of all that's transpired on and off the football field
The last-16 knock-out round kicks-off this week with Chelsea visiting Paris on Tuesday; Zidane to coach Real Madrid as manager in his first match in Europe
Factbox on the Real Madrid and Portugal forward who was voted FIFA Player of the Year on Monday.
Wolfsburg shock Real Madrid 2-0 to crown big European night.
Barcelona dismissed any notion they are a declining force when they won 2-0 at Manchester City on Tuesday to virtually guarantee their place in the quarter-finals of the Champions League for the seventh successive season.
Nemanja Matic's header ended Sporting's proud four-year unbeaten home run in Europe as Chelsea seized control of Champions League Group G with a 1-0 victory in Lisbon on Tuesday.
Photos from the Champions League matches played across Europe on Tuesday.