Rowntree led Munster to the URC title – their first trophy in 12 years – in his first season in charge.
Munster also secured top spot in the the URC last season, but the 53-year-old leaves after a disappointing start to the current campaign.
“We would like to thank Graham for his passion and dedication to Munster Rugby over the past five years, and I would like to wish him and his family the very best for the future on behalf of Munster Rugby,” said Munster chief executive Ian Flanagan.
“With the All Blacks XV coming to a sold-out Thomond Park this weekend and a number of big games on the horizon in November and December, our focus will be on continuing to support the coaches and the players for the season ahead.”