The Raptors announced on Twitter that Lowry would undergo surgery on Tuesday morning on his right wrist to remove "loose bodies."
"Aim to return for playoffs," the team added in its tweet without providing further information.
Toronto are currently fourth in the Eastern Conference standings and on course to reach the playoffs with a 35-24 record.
However, the absence of Lowry is a serious injury blow for Toronto as they attempt to go one better than last season when they fell to the Cleveland Cavaliers in the Eastern Conference finals.
"Not good. It was one of those things we didn't know it was as serious as it was," Toronto coach Dwane Casey said of Lowry's injury.
"That's why you get second opinions as he did. He decided to have it done now, hopefully to have some time before the playoffs to get some games in."
In his 11th season in the NBA, Lowry is averaging a career-best 22.8 points per game with 6.9 assists and 4.7 rebounds.
Lowry last played in the NBA All-Star Game on February 19, when he weighed in with 19 points and made five of nine three-point attempts.