Following Wednesday's 3-0 Champions League defeat by Paris St-Germain, the club's board has decided to dismiss the Italian, who replaced Pep Guardiola at the start of last season.
Ancelotti, 58, helped Bayern win the Bundesliga last term, but they only reached the last eight of the Champions League and the German Cup semi-finals.
Assistant boss Willy Sagnol will take temporary charge.
Bayern are third in the German table, three points behind Borussia Dortmund, with four wins, one draw and one defeat from their first six league matches. They next play away to Hertha Berlin on Sunday (14:30 BST).
"The performance of our team since the start of the season did not meet the expectations we put to them," said Bayern's chief executive Karl-Heinz Rummenigge.
"I would like to thank Carlo for his cooperation. Carlo is my friend and will remain my friend, but we had to make a professional decision. The game in Paris clearly showed that we had to draw consequences."
Former Chelsea, PSG, Real Madrid and AC Milan boss Ancelotti has won the Champions League three times - with Milan in 2003 and 2007, and with Madrid in 2014.
That return makes him the joint most successful manager in European Cup history, along with former Liverpool boss Bob Paisley, who also won three titles, in 1977, 1978 and 1981.
Ancelotti also led Milan to the Champions League final in 2005, but the Italian side were beaten on penalties by Liverpool, despite having led 3-0 at half-time.
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