Philip Nolan and Niels Giffey each added 10 points for the Huskies (17-4, 5-3 American Athletic Conference), who won for the sixth time in seven games.
Danrad Knowles had 10 points and eight rebounds to lead Houston (11-10, 3-5), which has lost five of its last six.
Connecticut jumped out to an early 18-3 lead and never looked back. The Huskies led by 29 points at halftime and stretched it out in the second half.
Connecticut was ranked 17th in the nation when it lost at Houston 75-71 on New Year's Eve in the conference opener for both teams. The Huskies fell behind by 21 points in the first half of that game.
UConn flipped the script in this one. Houston didn't get a point until a jumper by L.J. Rose, 3 minutes into the game. Napier and Lasan Kromah each had six points as the Huskies sprinted out to a 15-point lead less than 6 minutes into the game.
A three-point play by little-used freshman Kentan Facey put the Huskies up by 21 points, 31-9, equaling Houston's largest lead in the first game. A 3-pointer by Ryan Boatright just before the halftime buzzer gave the Huskies a 51-22 lead at the break.
Boatright opened the second half with another 3 to give UConn a 32-point lead and Houston never really challenged the Huskies in the second half.
UConn led by 40 when reserve Leon Tolksdorf hit a 3-pointer with 4 minutes left.
Nolan, who came into the game averaging 3.5 points, had all 10 of his points in the first half, when the Huskies hit 54 percent of their shots.
They shot 43 percent for the game, while holding the Cougars to 27 percent. UConn also outrebounded Houston 55-40 despite being without their top rebounder, DeAndre Daniels.
Daniels who sprained his right ankle in the first half of the Huskies win Saturday at Rutgers. He came back to play in the second half of that game, but was in a walking boot all this week, and did not practice. He had played 52 straight games before Thursday night, and had started the last 50.
TaShawn Thomas, who scored 23 points in the teams' first meeting, had just four in this one.
Daniel House was playing in just his fourth game back since undergoing knee surgery on Dec. 2 and had five points in his first start since the injury. J.J. Richardson, saw his first action since mid-December and had six points.
LeRon Barnes, who sat most of the first half in foul trouble, left the game less than 3 minutes into the second half after coming down hard on his head underneath the UConn basket while trying to block a shot.
UConn had won five of its last six games since the trip to Texas, which also included a loss at SMU.
Napier passed the 1,600-point plateau and passed Jeff Adrien into 14th place on the school's all-time scoring list. He is the only player in school history with 1,500 points and 500 assists.
This was the fourth 9 p.m. start for the Huskies this season. They were 0-3 in the others.