Borussia Dortmund are already seven points clear this season and looks a far better bet for the title than Niko Kovac's disjointed team.
Bayern, the six-time defending champion, did not give the extent of Neuer's injury, nor an indication of how many games he will miss.
Other than them, AS Roma and Ajax also reached the round-of-16 of the Champions League on Tuesday.
Bayern fell seven points behind Dortmund, which remains the only unbeaten team in the Bundesliga.
Dortmund, which had a four-point lead, moved seven points clear of Bayern and stayed four clear of second-placed Borussia Moenchengladbach, which defeated Werder Bremen 3-1 away.
Bayern started the season with seven wins across all competitions but have dropped to fifth after seven rounds of the league, four points behind Dortmund.
Bayern were on a roll after starting the season with seven wins in all competitions, but the team dropped points with a 1-1 draw against Augsburg on Tuesday before losing at Hertha Berlin 2-0 on Friday.
The former FC Barcelona and Bayern Munich boss added that he "always had the curiosity of trying out" the possibility of leading a national team.
Vidal, who has played for Juventus and Bayern Munich, wishes to win the Champions League with FC Barcelona as he signs a three-year contract.
The 31-year-old player joined Bayern from Juventus in 2015 and won the Bundesliga title in each of his three seasons in Bavaria.
Germany and Bayern Munich's goalkeeper Neuer denied there was any ill-feeling amongst the team towards Ozil after the Arsenal star announced his shocking retirement from international football.
Lewandowski has scored 106 goals in 126 Bundesliga games for Bayern since switching from league rival Borussia Dortmund in 2014. He helped the team win the league each year, chipping in 29 goals this season.
Bayern Munich end their season with the league title only as Frankfurt astonished the Bundesliga champions 3-1 to win the German Cup final at Berlin.
Karim Benzema was a surprise addition to the starting lineup in the Champions League semifinal against Bayern Munich.
Real Madrid conceded early again at home and barely held on for a draw 2-2 against Bayern in Tuesday's semifinal match, advancing 4-3 on aggregate.
Madrid relied on Marcelo and halftime substitute Marco Asensio to produce a comeback after Bayern had gone in front through Joshua Kimmich.
Madrid, who have been handed Europe's best have proved themselves worthy of being at the stage and are two steps away from successfully defending their trophy for the third time.
Bayern Munich, which clinched its sixth consecutive Bundesliga title on Saturday, progressed to the final four of Europe's premier competition thanks to its 2-1 win over Sevilla in the first leg in Spain.
Bayern did it with five rounds to spare, allowing the team to focus on the Champions League and German Cup for the rest of the season.
FC Barcelona will take on AS Roma where as Sevilla will face German giants Bayern Munich in the quarterfinals of the 2017-2018 UCL season.
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