Allen was a perfect 11-of-11 at the free throw line while Rajon Rondo connected for 15 points and distributed 10 assists in the victory, which was a possible preview of a first-round playoff match-up.
Boston retained the fourth seed in the Eastern Conference and the Bucks held onto fifth, a half-game in front of Miami.
With 2:22 left in the contest, Pierce and Milwaukee's Jerry Stackhouse shoved each other and were given technical fouls, triggering a tirade by Bucks head Coach Scott Skiles. Skiles earned a pair of technical fouls and was tossed out of the game.
John Salmons led Milwaukee with 21 points and Brandon Jennings contributed 19 as the Bucks saw their four-game winning streak snapped.