Spain midfielder Alonso saw red after earning two second-half bookings in quick succession at the BayArena.
Having brought down junior German international Julian Brandt in the second-half, a tactical foul on Leverkusen’s star striker Javier Hernandez saw Alonso sent off.
It was the fifth time Alonso, who has played for Liverpool and Real Madrid, has been sent off in his club career and it was his first red in Germany.
“That wasn’t a yellow card,” said Bayern coach Pep Guardiola after seeing a replay of Alonso’s bodycheck on Hernandez.
“We struggled in the first half to put three or four passes together. If you can’t do that, it’s impossible to play,” added Guardiola.
“I think we did enough in the second half to win it, but it’s never easy in Leverkusen.”
The 45 year old is already annoyed with repeated questions following Monday’s announcement that he will coach Manchester City next season.
“No more questions on this topic, please,” he said tersely when asked if he finds it hard to remain focused on Bayern.
The result leaves Bayern eight points clear of second-placed Borussia Dortmund at the end of a week to forget for the Bavarian giants.
On Wednesday, Bayern strongly denied allegations midfielder Arturo Vidal was repeatedly drunk at last month’s training camp in Doha.
Both the club and player say they will sue magazine Sport Bild over the claim.
Vidal started against Leverkusen as Guardiola played a back three after injuries left him with only one fit centre-back in Holger Badstuber.
Despite having scored 19 goals in as many league games this season, Bayern striker Robert Lewandowski failed to convert either of his two shots at goal.
Leverkusen restricted the visitors to just nine shots overall to the hosts’ six.
Earlier, Pierre-Emerick Aubameyang, the Bundesliga’s top-scorer, had also failed to score in Dortmund’s uninspiring goalless draw at Hertha Berlin with Jose Mourinho watching.
Aubameyang, who has netted 20 league goals, had a rare off day in Berlin, managing just 11 touches in his 71 minutes and failed to create a single shot on goal.
The Gabon forward – Africa’s player of the year – was eventually hauled off by Dortmund coach Thomas Tuchel and was left scowling on the bench.
It was only the sixth time this season ‘Auba’ has failed to score in one of Dortmund’s league games.
The game failed to deliver as second-placed Dortmund remained ten points clear of Hertha.
Dieter Hecking’s Wolves had few answers as Klaas-Jan Huntelaar, Johannes Geis and new-signing Alessandro Schoepf netted for Schalke.
The result pushed them up to fourth as Wolfsburg drop to eighth.
Stuttgart are now up to 11th, five points from the bottom three, with their fourth straight league win in a bad-tempered 4-2 victory at Eintracht Frankfurt as both sides finished with 10 men.
Stuttgart raced into a 2-0 lead as Christian Gentner, then Daniel Didavi scored for the visitors before but the latter was shown a red card after picking up a second booking on 67 minutes.
Frankfurt captain Alex Meier pulled it back to 2-1 with 40 minutes left before Stuttgart pulled away with goals by defender Georg Niedermeier and Filip Kostic.
Eintracht defender Carlos Zambrano also saw red after being sent off 15 minutes from time for his second booking.
Frankfurt’s Szabolcs Huszti then made it 4-2 by scoring in the 90th minute.
Hannover remain rooted to the bottom of the table after their 1-0 defeat at home to Mainz as Spanish midfielder Jairo scored the first-half winner.
Ingolstadt won the Bavaria derby with a 2-1 win at home to Augsburg thanks to Moritz Hartmann’s winning penalty five minutes from time.
On Friday, Borussia Monchengladbach got back to winning ways with a 5-1 thrashing of strugglers Werder Bremen as teenage Danish defender Andreas Christensen, on loan from Chelsea, netted twice.
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