Thomas tossed for 268 yards on 22-of-36 efficiency and picked up 60 rushing yards for Virginia Tech (7-1, 3-1 ACC), which won its third straight since falling to Clemson in the conference opener.
David Wilson contributed 134 yards and a score on 17 carries and Danny Coale hauled down a career-high eight passes for 118 yards in the victory.
The Eagles (1-6, 0-4), meanwhile, dropped their third straight.
Chase Rettig passed for 181 yards with a touchdown and an interception while Rolandan Finch accounted for 145 total yards for Boston College.
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