The Poland frontman broke the offside trap to latch onto Thiago's through-ball before being hauled down by Burki as he tried to round the Dortmund goalkeeper.
Veteran wingers Arjen Robben and Franck Ribery also netted in Bayern's morale-boosting win before Wednesday's crunch Champions League quarter-final, first-leg, tie against Real Madrid.
"Lewy sustained a bruise, but the medical unit says it's no problem with regard to Wednesday", the Bayern boss told his club's website.
The battle between the mighty Bayern Munich and Borussia Dortmund takes place Saturday in the Bundesliga.
"I can guarantee today that we have not contacted or will contact any of these players".
Max Meyer set up Guido Burgstaller to give the home side an early lead, and Leon Goretzka made it 2-0 in the 23rd minute.
With seven games remaining, league leaders Bayern are now 10 points ahead of nearest challengers RB Leipzig and 15 points clear of fourth-placed Dortmund, who are battling with Hoffenheim for a direct Champions League qualification spot.
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"But he and Thomas Muller will both be fit for Real Madrid".
"So on Saturday we will give it all we have", said Hummels. "Of all those who may miss out, (defender) Marc Bartra seems to have the best chance (of playing)", Dortmund coach Thomas Tuchel said on Friday.
Schalke's scorer Leon Goretzka puts his arm on Schalke's scorer Daniel Caligiuri after the third goal during the German Bundesliga soccer match between FC Schalke 04 and VfL Wolfsburg in Gelsenkirchen, Germany, Saturday, April 8, 2017. "But it was balanced before his goal".
Fourth-placed Dortmund, who are 18 points behind Bayern, were second best throughout as Bayern turned on the style in front of their own fans.
"I'd have been surprised at anything other than this dominance and this result", Tuchel said in his press conference, according to their opponents' official website. But in this match, it was Bayern's old guys who got the job done. "We played very well. It's a bitter experience".
However you look at it, Bayern Munich are the favourites here at (1.65) with SportyBet, and we feel that backing the hosts is the way to go here.
"It will be a tough task". So far this season he has played in 31 of the team's 39 competitive games, contributing five goals and setting up four more.