The Germany international set up Mario Mandzukic for the opening goal prior to curling home a brilliant free kick before Stefan Kiessling netted a late consolation
The Germany international crossed for Mario Manduzkic to head the home side in front just before the break before he curled home a sublime free kick in the second half to secure the points and extend Bayern's unbeaten Bundesliga record to 50 matches.
Stefan Kiessling scored a consolation goal in injury time for Sami Hyypia's side, but Bayern remain on course to defend their title after moving 23 points clear of Borussia Dortmund following their 2-1 defeat to Borussia Monchengladbach.
Bayern made six changes to the side that drew with Arsenal in the Champions League in midweek, with winger Franck Ribery left on the bench by Guardiola.
Both teams traded chances early on, Arjen Robben drawing a fine low save from Bernd Leno after eight minutes, before Son Heung-Min missed a glaring opportunity to give Leverkusen a shock lead two minutes later.
The South Korean striker was slipped through by Kiessling, but sent his close-range shot narrowly wide of the post.
Defences were on top for much of the first half and only the fine reflexes of goalkeeper Manuel Neuer kept Bayern on level terms as he produced an excellent stop to tip Simon Rolfes' long-range drive over the bar.
But for all for their attacking initiative, Leverkusen were undone shortly before half-time as Mandzukic glanced Schweinsteiger's right-wing cross into the top corner.
And victory was all but ensured for Guardiola's men 10 minutes after the break when Schweinsteiger curled a marvellous free kick beyond a despairing Leno.
Bayern refused to take their foot off the gas and pushed on for a third, which would have arrived if not for Leno, whose diving save kept out a powerful Toni Kroos strike from distance.
Leverkusen pulled one back in injury time as Kiessling headed home from Roberto Hilbert's right-wing cross, but that proved to be little more than a footnote as Bayern moved within touching distance of the title and put the turbulence of former president Uli Hoeness' resignation and prison sentence behind them.