Napier, who had a team-high 18 points in the Huskies' opener last week, piled up 14 points, 11 rebounds and 10 assists against Yale (1-1).
A sluggish start allowed Yale's Jesse Pritchard to score a 3-pointer that tied the score 9-9 midway through the first half. But Niels Giffey four times in quick succession turned passes from Napier into 3-point shots for a personal 12-3 run.
With Yale's Anthony Dallier getting a 3-pointer of his own in the run, Giffey's barrage boosted Connecticut (2-0) into a 21-12 lead. His first shot came within 10:59 to go in the half and the fourth hit the net 77 seconds later.
Giffey added another 3-pointer in the first period as the Huskies led 39-24 at the half.
A quick 7-2 run had Connecticut up 46-26 2 1/2 minutes into the second half and the Huskies sailed in from there.
Connecticut shot 56.7 percent from the floor, including 11-of-17 (64.7 percent) from 3-point range. Omar Calhoun had a team-high 18 points. Giffey added 15 and Ryan Boatright matched Napier's 14-point game.
Yale's Justin Sears backed up his season-opening double-double with 17 points and 10 rebounds Monday.