"I told him, I'm going to get you back. I'm going to get you back for that,'" Waiters said afterward.
Waiters dropped 31 points as his squad, Team Hill, named for former NBA star Grant Hill, who selected the players, beat a team drafted by Chris Webber, 142-136.
Waiters answered Hardaway's bucket with a long 3, hitting the shot only after he used a crossover that made Hardaway fall to the floor.
The next possession, Hardaway nailed an ever longer trey.
"We were just trying to do a good job of getting the fans involved, said Hardaway, who had 36 points. "It was kind of dead in there and we wanted to start something."
Hardaway's 3-pointer from 33 feet out got All-Stars Kevin Durant and James Harden out of their courtside seats and cheering.
"Really, I would like to see more team play, a little bit more ball movement, as opposed to Gladys Knight over here and the Pips over here style of basketball," said Team Hill coach and Indiana Pacers assistant Nate McMillan. "But it was entertaining. I thought the shots they made were big shots. Both of those guys were hot."
Andre Drummond won the game's MVP honors for scoring 30 points and grabbing 25 rebounds.
But the night belonged to Hardaway and Waiters.
Utah Jazz point guard Trey Burke said he'd seen Hardaway hit six or seven in a row before while the two were playing at Michigan.
"Just give him the ball and get out of the way," said Burke, who struggled to hit his shots, going 3 of 13, but dished out six assists. "That's what kind of game it was for both of them tonight."
"That was a sight," Burke said. "That's what it's about."