The hosts did not have it easy against a determined Leverkusen side, who drew level before the defender stepped up to give his team a priceless three points.
Mats Hummels netted his first Bundesliga goal for Bayern Munich as Carlo Ancelotti’s side battled to a 2-1 victory over Bayer Leverkusen on Saturday.
The Germany international returned to the club from fierce rivals Borussia Dortmund in the close-season and made a decisive intervention at the Allianz Arena to end a poor run of form for his team.
Ancelotti kept faith with just four of the starting XI from the shock 3-2 defeat at Rostov in the Champions League in midweek, and the fresh faces – including Hummels – managed to help end their three-match winless run in all competitions.
Surprise leaders RB Leipzig had increased their advantage over Bayern to six points with a 4-1 win at Freiburg on Friday, but the four-time defending champions were able to respond despite being below their best here.
Thiago Alcantara – one of the quartet who did start in Russia – put the home side ahead with a close-range header on the half-hour mark but the lead was short-lived, Hakan Calhanoglu equalising superbly five minutes later after a slick one-two with Julian Brandt.
Hummels’ powerful header from a corner early in the second period restored the lead and – unlike against Rostov – it was one they would not relinquish, despite controversy late on with Javi Martinez escaping two strong penalty shouts from Leverkusen.
Bayern’s defence had come in for fierce criticism following the loss at Rostov and they were almost breached in the second minute when Admir Mehmedi flashed a low shot narrowly past the post.
Thomas Muller prodded wide as Bayern responded, before Robert Lewandowski waited too long to shoot having been sent through by Xabi Alonso and Joshua Kimmich headed straight at Bernd Leno.
Bayern huffed and puffed for much of the opening half-hour but found themselves ahead as Kimmich laid the ball off for Philipp Lahm, whose effort was parried up into the air by Leno where Thiago was on hand to nod home from a couple of yards out.
And it was almost a second two minutes later, Leno producing a superb sprawling save to deny Lewandowski from David Alaba’s cut-back.
The importance of that stop was underlined shortly afterwards as Leverkusen equalised in sublime style.
Calhanoglu cut in from the left, exchanged passes with Brandt and lifted an excellent finish beyond Manuel Neuer into the top-right corner.
Bayern began the second period with greater purpose, Leno keeping out Douglas Costa but it was a temporary respite as Kimmich swung in a right-wing corner and Hummels thumped in a header.
Roger Schmidt summoned Kevin Volland and Javier Hernandez from the bench in an immediate response and the former came close to an equaliser in the final 10 minutes.
After lifting the ball over Neuer, Volland’s attempted header from a tight angle close to the post appeared to be stopped by the hand of Martinez, who was also perhaps fortunate not to concede a spot-kick for bundling into Aleksandar Dragovic in stoppage time as Bayern escaped with all three points.