The 28-year-old Brazilian required the operation to mend a torn meniscus after he limped off the pitch late in Tuesday's home draw with Eibar.
LaLiga: Barcelona dealt with injury blow as midfielder Philippe Coutinho set to undergo knee surgery
Coutinho's loss adds to a long list of injuries including Lionel Messi, with the club sixth in LaLiga seven points off leaders Atletico Madrid.
Ronald Koeman said Messi will remain crucial for Barcelona even if he doesn't play as much or as well as in the past.
Barcelona toasted the resignation of Josep Maria Bartomeu as president on Tuesday by beating Juventus 24 hours later in the Champions League. But not everything has changed.
FIFA World Cup 2022 qualifiers: Roberto Firmino brace powers Brazil to thumping victory over Bolivia in opening match
Barcelona playmaker Philippe Coutinho and Paris Saint-Germain defender Marquinhos also got on the scoresheet while star forward Neymar set up two goals in a totally one-sided encounter that sent Brazil top of the South American qualifying table.
While other players including Jordi Alba and Philippe Coutinho arrived for the session, Messi failed to appear at the Joan Gamper training complex for the session
LaLiga: Philippe Coutinho returns to Barcelona after year-long loan spell with European champions Bayern Munich
Coutinho netted 11 goals, creating nine more, in 38 games for Bayern, including scoring twice in the 8-2 mauling the Germans handed his club Barcelona in the jaw-dropping Champions League quarter-final.
This Bayern Munich's 19th consecutive victory in all competitions, and a 28th game unbeaten for Hansi Flick's side. They have now scored 39 goals in nine Champions League outings this season.
Champions League: Bayern Munich boss Hansi Flick mulls starting Ivan Perisic or Philippe Coutinho for last 16 second leg
Bayern host Frank Lampard's Chelsea at the Allianz Arena in the last 16, return leg holding a 3-0 advantage after routing the Blues at Stamford Bridge last February before the competition was halted due to the coronavirus pandemic.
Dodgy transfers, boardroom mayhem, managerial merry-go-round: Barcelona have been in disarray for a while, the cracks are deepening now
Barcelona may be just four points behind Real Madrid in the league but the club has all but conceded defeat while dropping six points in last four games.
Bayern Munich midfielder Philippe Coutinho undergoes minor surgery on right ankle, set to begin rehab in two weeks
Coutinho, on loan from Barcelona for one season, could be back fit for the remainder of the Bundesliga campaign, which has been suspended since mid-March due to the coronavirus outbreak
Bayern Munich fired in three goals in opening 15 minutes en route to a 6-0 demolition of Hoffenheim in a game interrupted for 20 minutes over an offensive banner unfurled by visiting fans
Bundesliga: Bayern Munich's Philippe Coutinho scores hat-trick in 6-1 rout of Werder Bremen; Borussia Dortmund win against Mainz
Bayern Munich's man-of-the-match Coutinho, who also helped set up two more goals, delivered at just the right time with the Bavarians, struggling to find their rhythm under interim coach Hansi Flick
Philippe Coutinho scored one goal and helped set up another as Brazil beat South Korea 3-0 in a friendly on Tuesday to give the five-time world champion its first win in six games.
Inter Milan and Manchester United interested in Bayern Munich's out-of-favour star Thomas Mueller, says report
Reports in Germany believe Inter Milan and Manchester United are interested in signing former Germany star Thomas Mueller, who has lost his starting place at Bayern Munich.
Bundesliga: 'I'm satisfied with everything but our goal tally', says Bayern Munich president Uli Hoeneß about team's lacklustre start to season
Saturday's 2-2 draw at struggling Augsburg followed a 2-1 loss at home to Hoffenheim and ensured that Bayern have dropped points in half of its league games so far
On Wednesday, Thomas Mueller said he is 'unhappy' about starting the last five Bayern games on the bench, amid reports he wants to leave in January.
Champions League: Bayern Munich's record signing Lucas Hernandez says current transfer fees are unbelievable
Lucas Hernandez, the most expensive signing in Bayern Munich's history, says "unbelievable" fees are currently being paid on the transfer market, putting pressure on the players concerned to justify the astronomical sums.
Bayern Munich's Robert Lewandowski became the first player in Bundesliga history to score 10 goals in the first six games to seal a 3-2 victory at bottom club Paderborn.