Hartford (4-8) led by 16 at intermission, 35-19, as Sacred Heart had several long stretches without baskets. The lead reached 20 points with 10:27 to go on a Jalen Ross free throw.
Sacred Heart made a 14-2 run, punctuated by Cane Broome's 3-pointer, to draw to within four points with 4:18 remaining. But Hartford's Justin Graham hit a jumper on the next possession, and then Thomas drilled a 3 with 1:15 left to make it a five-point game.
Sacred Heart missed its next three shots - all 3-point attempts - and Hartford made 6 of 8 free throws to ice it.
Graham finished with 13 points and J.R. Lynch added 12 for Hartford.
Broome and Jordan Allen had 15 points apiece for Sacred Heart (1-8).