Seguin, the second-overall pick in the 2010 NHL draft, scored the game's first two goals and added a third with 5 minutes remaining in the second period for a 4-0 Bruins lead.
Milan Lucic added two goals and an assist, David Kreji contributed a goal and two helpers and Gregory Campbell also found the net for Boston, which earned its first back-to-back wins of the season after going 3-7-0 in October.
Thomas turned aside all 25 shots he faced, notching his first shutout of the season and 27th of his career.
Rookie Maple Leafs goalie Ben Scrivens was shelled in his second NHL game, yielding five goals on 14 shots before being pulled with 5 minutes left in the second period.
Jonas Gustavsson relieved and stopped 4-of-6 the rest of the way.