The 25-year-old Alcacer joined the German leaders on a season-long loan in August, and Dortmund had the option of making the deal permanent.
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 Spanish striker, who joined Dortmund from Barcelona in the offseason, scored the winner to give Lucien Favre's men three vital points in the league.
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.
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.
Frankfurt, which had twice come from behind to pull level, is two points behind Bayer Leverkusen, which occupies the last Champions League qualification spot.
Reus was handed the captain's armband 259 days after the German forward sustained a cruciate ligament injury in the German Cup final.
Stoeger was sacked as Cologne coach the previous Sunday after his side failed to win any of its opening 14 Bundesliga games of the season.
The hosts let a four-goal lead slip away after Schalke ran riot after half-time to salvage a draw in the dying minutes of a thriller match.
Hertha's starting lineup linked arms and took a knee on the pitch, while Pal Dardai's coaching staff, general manager Michael Preetz, club officials and substitutes took a knee off it before kickoff.
Ancelotti acknowledged he would face criticism for his lineup but remained defiant after the game against PSG in the Champions League.
Goals from Robert Lewandowski and Arjen Robben counted for little as Bayern dropped points for the second time in six games following a lacklustre performance.
While the Colombian midfielder made his first league start for Bayern, American teenager Weston McKennie did likewise for the home team.
Robert Lewandowski marked his 100th league appearance for Bayern with his 81st and 82nd goals, which came on the first day of the 184th beer festival.
Ancelotti, who has been irritated by questions over his rotation policy, faces added pressure after being outshone by Hoffenheim's coach Julian Nagelsmann.
Counterpart Carlo Ancelotti was left pondering how his side lost after 23 efforts at goal.
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