Boston has won each of its last eight meetings with the Maple Leafs, who were riding a three-game victory streak coming into the contest.
Seguin gave Boston a 2-1 lead midway through the second period and David Krejci's backhander with 1:57 left in the middle stanza boosted the Bruins' advantage.
Jay McClement brought the Maple Leafs within one with 5:08 to play in regulation, but Seguin decided the outcome by scoring into an empty net with 45 seconds to play. He ran his season goal total to seven.
Boston ended a two-game skid with Anton Khudobin making 25 saves. Khudobin, lightly used during a four-year NHL career, appeared in his fifth game of the season.
Ben Scrivens allowed three goals on 24 shots.