Carl Soderberg snapped a 3-3 tie late in the second period and Patrice Bergeron supplied a goal with two assists as the Bruins took a fourth victory in five games.
Chad Johnson earned the win with 34 saves.
Kyle Okposo logged a goal and two assists for the Isles, who dropped a third straight.
Kevin Poulin started in net but was pulled early in the third period after stopping just 20-of-26 shots.
Evgeni Nabokov, playing in his first game since coming off injured reserve list, turned aside the only shot he faced.