Robert Lewandowski scored twice in the space of three minutes as Werder's dogged resistance was belatedly broken by the Bundesliga champions.
Muller came on after the 72nd-minute opener and laid on Lewandowski's second but was unhappy with the role he played. Ancelotti, however, explained his desire to control central midfield while retaining the attacking threat of wingers Arjen Robben and Franck Ribery was behind his decision.
"We tried to plan the game using the wide areas more and to have more possession in the middle," he told a post-match news conference.
"For this reason, Thomas didn't start the game. He went in during the second part of the game and did well.
"It was only a technical decision."
Bayern captain Manuel Neuer had a largely untroubled afternoon as he made his return to competitive action after breaking his foot in April.
The Germany goalkeeper has been left out of Joachim Low's squad for the forthcoming World Cup qualifiers against the Czech Republic and Norway, but Ancelotti insists Neuer is unconcerned by this as he continues to build his fitness.
"I didn't speak with Low but he took this decision which is Manu [staying] here," he said.
"We have no problem, he has no problem and I think also the national team has no problem.
"He can train here with us and use these 15 days to improve his condition. He is already in a good condition."