The Fighting Irish guards got more aggressive in the second half, penetrating against the Red Storm defense to get their teammates going.
After shooting 28 percent from the field in the first half, the Irish shot 68 percent in the second en route to a 66-40 victory Tuesday night.
Grant had 21 points and eight assists, Atkins added 15 points and seven assists and the two had just one turnover apiece.
"Our guards ran the whole building tonight," Notre Dame coach Mike Brey said. "They probably took tickets, sold popcorn. When our guards are playing like that, I just sit down and shut up and let them do whatever they want. They were fabulous to watch."
The Fighting Irish (23-7, 11-6 Big East) ended a three-game losing streak to the Red Storm (16-13, 8-9), who lost for the fifth time in six games.
Brey and St. John's coach Steve Lavin both said they didn't get a good look at what happened. Lavin said his assistants told him the two started talking while JaKarr Sampson of St. John's was shooting free throws seconds earlier. Lavin said Pointer told him "he just lost his cool."
Brey said Biedscheid told him he was defending himself.
"He felt it started with the other guy and he defended himself. But under the rule, if you do throw a punch you're ejected," Brey said.
Lavin said Pointer would be suspended for the team's regular season finale.
"Dom apologized for losing his composure and will serve his penalty by missing the final game against Marquette," Lavin said. "We have to demonstrate more maturity than we did tonight. We want to play with intensity but also use intelligence in order to play a winning brand of basketball."
Amir Garrett of the Red Storm was ejected for leaving the bench. The Big East said it would review what happened.
"Coach Lavin, his staff and team have continued a tradition of integrity associated with our men's basketball program and will deal with this isolated incident accordingly," St. John's said in a statement released Wednesday.
Grant kept the Irish in the game early, scoring 10 of Notre Dame's first 19 points as St. John's tried to open a lead. The Red Storm went ahead 26-19 when Pointer hit a 3-pointer to cap an 8-0 run with a minute to go in the first half.
But then Atkins hit a 3-pointer to cut the lead to 26-22 at halftime, and Notre Dame opened the second half on a 29-8 run to take control.
"We got some in transition where they weren't set. That helped us," Brey said.
Notre Dame, which was 1 of 9 from 3-point range in a 67-63 loss to the Red Storm in January, hit three 3-pointers during that run and was 8 of 17 for the game. The Irish went to a zone defense in the second half and held the Red Storm to 18.5 percent shooting.
Lavin said the difference was the Irish took high-percentage shots in the second half, and credited Grant and Atkins.
"They just carved us up, just sliced us up for easy baskets," he said.
After being held to four points in the paint in the first half as St. John's blocked six shots, the Irish scored 20 points in the paint in the second half.
"Very aggressive, attacking the rim," Lavin said. "That was really the difference. I thought Grant was big for them throughout the game."
Grant said the Irish were sluggish in the first half.
"Once we got out and running in the second half, we did pretty well," he said.
Brey said the Irish going to the zone in the second half was key.
"The zone really slowed them down. They weren't as bouncy. Because when we got back and played zone it made them take almost too much time and they got out of attack mode a little bit," Brey said.
Jack Cooley, who only played 15 minutes and was held scoreless Saturday against Marquette because of an illness, went 0 for 2 in the first half against St. John's before scoring 12 points in the second half. He had 13 rebounds in his final home game.
"You knew it was coming," Brey said.
Sampson had 12 points and Phil Greene added 10 for the Red Storm, who finished with 10 blocked shots.
Greene said the Red Storm settled for jump shots too often in the second half.
"You have to play through the paint. They went to the paint and we didn't," he said.
Information from ESPN.com's Andy Katz and The Associated Press was used in this report.