Leverkusen are the only club to beat the Bundesliga leaders this season after winning 2-1 in Munich in October, but they fell behind on Saturday evening when Mario Gomez poked home in the 37th minute.
Simon Rolfes headed in at the far post from a corner in the 75th minute to give Leverkusen hope of coming away with a point but Wollscheid unwittingly diverted Bastian Schweinsteiger's free-kick into his own goal three minutes from time.
It was perhaps a touch cruel on the hosts as Bayern maintained their 20-point gap at the top of the standings over reigning champions Borussia Dortmund, who thumped Freiburg 5-1.
The mid-table side took the lead in the 28th minute through Jonathan Schmid although two goals from Robert Lewandowski either side of Nuri Sahin's strike put the Westphalians 3-1 ahead before the interval.
Turkey international Sahin got his second of the game in the 72nd minute before substitute Leonardo Bittencourt completed the rout in the 78th minute - just a minute after being introduced.
Nuremberg piled more misery on Schalke with a convincing 3-0 win at the Frankenstadion.
After being eliminated from the Champions League by Galatasaray in midweek, Schalke saw their bid for a top-four Bundesliga finish suffer a setback.
Markus Feulner put Nuremberg ahead before half-time with further goals from Alexander Esswein and Mike Frantz earning Michael Wiesinger's side all three points, moving them 10 points clear of the drop zone.
Augsburg boosted their survival hopes with a 1-0 victory in Hamburg which reduced the gap to 15th-placed Stuttgart to just five points and dented the home team's hopes of playing in Europe next season.
Jan-Ingwer Callsen-Bracker scored the only goal of the game in the eighth minute, while Hamburg's woes were compounded by a red card shown to Maximilian Beister late on.
Werder Bremen's troubled season continued as they were held to a 2-2 draw at home by bottom club Greuther Furth whose new coach Frank Kramer had an encouraging first game in charge.
Aaron Hunt scored two penalties for Bremen in-between strikes from Stephan Furstner and Thanos Petsos for Furth, who were playing under new coach Frank Kramer for the first time.
Hoffenheim are nine points adrift of safety after a goalless draw at home to Mainz.
On Friday, Ivica Olic netted a 51st-minute equaliser to rescue a 1-1 draw for Wolfsburg at home to Fortuna Dusseldorf.
Saturday's Bundesliga Results
Friday's Bundesliga Results