The club said Lowry sustained "an acute back spasm" and would be reevaluated Tuesday.
The injury to Lowry made a tough night even more difficult.
While the Raptors were working overtime to beat the Nets 114-113, the Miami Heat were resting for their game against Toronto on Tuesday night at the Air Canada Centre.
Lowry hit the court hard on a play under the basket late in overtime Monday. He had trouble getting to his feet and when he did, his legs buckled. He was carried to the dressing room and then taken for x-rays.
"I think (the injury is) more of a bruise than anything else," Raptors coach Dwane Casey said.
The Raptors (28-10) led by 10 points with 4:40 to play in regulation and won in overtime when DeMar DeRozan, who had 35 points, made a free throw to complete a three-point play with 26 seconds left.
"I'm always optimistic," DeRozan said about Lowry's injury. "I'm always tough on him. He's extremely tough, so I hate to see any type of injury. Hopefully it's nothing serious. That's all we can hope for. I don't want to think too much about it. He fell. He fell hard and as long as nothing is broke or anything like that then he should be fine."
The Raptors have won five games in a row overall and 10 straight over the Nets. They will have to play a better game against the Heat.
"We had too many defensive breakdowns," DeRozan said. "They took advantage of it. I think they hit four 3s in a row that got them back in the game. We can't have lapses like that, especially four 3s, and they were right back in the game and we made it tough on ourselves. We win in overtime. We had to fight being down, but we figured it out."
The Heat (22-17) took Monday off after defeating the Utah Jazz 103-102 on Sunday.
"We've pushed the limits a little bit and guys need some rest," Heat coach Erik Spoelstra said. "And then we need to gear up and focus on Toronto. That's it. Get up there, get a good night's sleep."
The Heat have been on a 6-2 surge in a span in which they have played seven of eight games at home. Starting Tuesday, they will play 11 of 14 on the road.
After winning a season-best four games in a row, the Heat are five games above .500 for the first time this season.
"We're road warriors, man," Heat forward James Johnson said. "Our road record (11-8) is better than our home record (11-9), so we're just going to keep doing what we're doing, staying together, being confident, feeding energy to guys and going from there, one game at a time, one stop at a time. We're trying to bring a little heat out there."
"The funny thing about it is we've been better on the road so hopefully we can keep it like that," guard Wayne Ellington said. "Eleven of next 14? It's gonna be tough. It's always tough playing in somebody else's house, but that's when we come together, and we show what we're made of."
"Yeah, it's weird that our away record is better than our home record," Miami center Hassan Whiteside said. "We've got some talented teams coming up."
In the win over the Jazz Sunday, six Heat players scored in double figures, and no player had more than 16 points.
"We are a team that has strength in numbers," Spoelstra said. "But eventually guys start to emerge, as well. And when we do have a balanced attack, everybody will feel involved and everybody can be a threat. There will be different guys on different nights.
"That's probably when we're at our best. But like I said, guys can grow and emerge into bigger roles as the season goes on and guys gain confidence."
The Raptors, meanwhile, will play five of their next six games at home, where they are 14-1.