Crawford, the league's Sixth Man of the Year, connected on a 3-pointer from the left wing to put the top-seeded Tigers (30-4) up 78-76 with 2:44 remaining. He also had a jumper and a pair of free throws in a 9-0 run by Memphis soon after that finally put the game away.
Daveon Boardingham scored 19 points and Jonathan Mills had 15 points and 17 rebounds for second-seeded Southern Miss (25-9), which nearly clinched an automatic bid to the NCAA tournament. Instead, the Golden Eagles must hope to get their second straight at-large bid on Sunday.
Dwayne Davis hit one of two free throws after Crawford's 3-pointer, and Thomas and Crawford then hit back-to-back jumpers for Memphis. Jackson then stripped Davis and ran out for a two-handed slam to make it 84-77 with 44.2 seconds left.
After letting Southern Miss come back from seven down in the final minute of regulation by missing free throws, Memphis made enough to close it out in double overtime.
The Golden Eagles were unable to take advantage of a chance to take the lead late in regulation after Shaq Goodwin was called for a flagrant foul when his right arm swung and inadvertently connected with Mills' cheek. Mills missed one of two free throws with 1:59 left,
Crawford, the star of Memphis' first two tournament wins, immediately expanded the Tigers' one-point lead with back-to-back 3-pointers to make it 60-53 with 38.3 seconds left in regulation.
Brooks answered right away with his own 3 at the other end, and Mills had two straight putbacks—the second after Geron Johnson missed the front end of a 1-and-1. Joe Jackson also missed the front end of a one-and-one with 4.4 seconds left, and Watson zipped to the opposite end to make a runner at the buzzer and tie it at 62.
Replays showed the ball leaving Watson's hand with one-tenth of a second left on the clock.
Watson also had a chance to win the game at the end of the first overtime, but his turnaround jumper from the left wing was after the buzzer and off-target. Jackson made a jumper from the left elbow with 11.2 seconds left to tie it at 72.
Neither team led by more than five until the final minutes of regulation, after Crawford's second straight 3-pointer.
Even against Memphis' bigger front line, the Golden Eagles were able to get inside for easier baskets and outscored the Tigers 50-22 in the paint. At the other end, the Tigers couldn't solve the Southern Miss zone enough to pull away without Crawford knocking down outside shots with regularity. Crawford had made 19 3-pointers in Memphis' last three games, but he started out 1 for 7 from 3-point range and didn't get going until the final 3 minutes of regulation.
He still came up with some of the biggest shots of the game and was named the tournament MVP.
Jackson added 22 points and Adonis Thomas had 18 points and eight rebounds for Memphis, which is 18-0 as the No. 1 seed in the Conference USA tournament and has won the title all six times.
Southern Miss had all five starters score in double figures, getting 16 from Davis, 11 from Watson and 10 from Brooks. The Golden Eagles haven't won a league tournament title since 1952 in the Gulf States Conference.