The Huskies (5-1) hit their final eight attempts from behind the arc Sunday to rally for a 73-62 victory.
Niels Giffey came off the bench to score a career-high 15 points and grab eight rebounds for UConn and Shabazz Napier had 15 of his 19 points in the second half.
Omar Calhoun added 14 points. The three players combined to go 9 of 16 from 3-point range. The team finished 10 of 22.
"(Stony Brook) packed it in, packed it in, they dared us to shoot 3s," said UConn coach Kevin Ollie. "Once we started getting in and understanding our offense and drawing two and taking an advantage, we started kicking it out and our guys were wide open."
Dave Coley led Stony Brook (4-2) with 15 points and Tommy Brenton added 14.
The Seawolves led 33-26 early in the second half after a 10-0 run that overlapped with halftime.
"We came out with great energy in the first half and we were winning, so there was no reason not to think we can't do it again," Brenton said. "I think this is a great learning experience."
The Huskies chipped away at the deficit, tying it at 39 with 11:40 to play on a jumper by DeAndre Daniels.
Back-to-back 3-pointers by Napier and Giffey put UConn up 45-39. That started the run of consecutive makes from behind the arc by the Huskies. A four-point play by Napier put UConn up 61-47 with just over 4 minutes left.
"As soon as I made that four-point play I felt it was our ballgame," Napier said. "I always feel like it's our ballgame, but that right there, I felt everybody else got excited and enthusiastic and that always gives you that effort to win that game."
Stony Brook made just five of its 18 3-point attempts and shot just 38 percent from the floor.
Coley opened the game with a 3-pointer and the Seawolves jumped out to an early 10-2 lead.
The Huskies missed 11 of their first 12 shots from the field and trailed 14-8 midway through the first half. Napier, UConn's leading scorer, didn't take a shot until almost 13 minutes into the game, when his layup cut the deficit to 15-14.
Daniels' putback gave the Huskies their first lead at 19-17.
But Stony Brook scored the last eight points of the half. Anthony Mayo blocked a 3-point attempt by Ryan Boatright just before the buzzer and the Seawolves carried a 31-26 lead into the break.
The Huskies shot just 32 percent from the field in the first half, but moved to 64 percent in the second.
This was just the second home game for the Huskies, who were coming off their first loss of the season to New Mexico in the Paradise Jam final in the U.S. Virgin Islands.
Stony Brook outrebounded Connecticut 38-35. The Huskies have been outrebounded in every game this season, and were averaging almost nine fewer rebounds than their opponents.
Stony Brook was averaging 41 rebounds per game. It was led by Jameel Warney's 11 boards. He also had eight points.
"I thought we could be plus-12 on the backboard going into the game," said Stony Brook coach Steve Pikiell, who like Ollie is a former UConn point guard. "So to be only plus-three was very disappointing."
Connecticut played without its top reserve, Holy Cross transfer R.J. Evans. Evans sprained his collarbone and is expected to miss about two weeks. The graduate student, in his final year of eligibility, has been a steadying presence for the Huskies, averaging about six points.
Giffey said without Evans, he felt he needed to step up.
"There are a couple of guys on this team who are like me," Giffey said. "We might not always be the big-time scorers, but we're glue guys. We keep everything together. Me and R.J. is one of those guys."
The Huskies improved to 5-0 against Stony Brook. Connecticut hasn't lost to a nonconference opponent in its on-campus arena since falling to Detroit Mercy in the 2001 NIT.
Stony Brook was looking to go 5-1 for just the second time in program history. The first came in 2009.
But the Seawolves were playing their second game in two days after beating Canisius at home on Saturday 82-75.
"We played a hard-fought game yesterday," Pikiell said. "And then to jump on the bus today and come up here wears on you a little bit. Hopefully this will help us when we move into our conference tournament."