Fans mobbed the floor when things ended, swarming a team that looked cooked about an hour earlier.
After rallying to tie, the Cougars caught fire in the extra period. They hit their first four shots, including a pair of 3-pointers by Marquise Pointer to take a 75-69 lead. Northeastern (23-10) could not come back.
The Cougars (26-7) appeared done early in the second half, trailing 42-25 after Vasa Pusica's 3-pointer with 17:27 to go. That's when Charleston ramped up the pressure - it forced 14 turnovers the second half - and tied it at 65-all on Chealey's layup with 10.1 seconds to go.
Charleston got the ball back with the chance to win in regulation, but Chealey's long 3-pointer hit off the front of the rim.
Jerrell Brantley gave the Cougars their first lead of the game, 67-65, in overtime before Pointer's first 3 gave Charleston the lead for good. Two minutes later, Pointer did it again as the large, loud crowd at the North Charleston Coliseum exploded in delight.
Northeastern's last chance disappeared when Pusica lost the ball out of bounds on a drive with 40 seconds to go. Chealey closed things with four foul shots to send Charleston back to the NCAAs for the first time since John Kresse led the school to four appearances in six seasons from 1994-99.
Kresse was seen on the arena video boards screaming and leading cheers down the stretch.
Pusica had 30 points to lead the Huskies, who saw their nine-game winning streak ended. Shawn Occeus added 19 points.
Grant Riller scored 20 points for Charleston, 14 of those after halftime. Brantley finished with 18.
Northeastern: The Huskies were poised and prepared in the opening half, but fell apart after the break. They turned the ball over 15 times in the second half and overtime to fuel Charleston's rally.
College of Charleston: The Cougars finally closed the deal after missing out a year ago in their first CAA Tournament finals in their home city. A team that appeared flustered and out of sync the first 22 minutes turned up the pace and ran past Northeastern. ... Charleston's lone NCAA Tournament win came in 1997 when they took down then-ACC power Maryland before losing to eventual champion Arizona.
Northeastern, which shared the regular-season crown with Charleston, will see if it will get an invite to a postseason tournament.
College of Charleston awaits its NCAA Tournament seeding.
More AP college basketball: https://collegebasketball.ap.org and https://twitter.com/AP_top25
Copyright 2018 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.