The 31-year-old American was at 13 under after 36 holes and had yet to tee off in the third round.
"I received exciting news a short time ago that my wife Kandi has gone into labor with our first child," Mahan said in a statement. "Kandi and I are thrilled about the addition to the Mahan family and we look forward to returning to the RBC Canadian Open in the coming years."
The sudden departure now puts the spotlight on John Merrick, who finished the second round two strokes back of Mahan after tying the course record with a 62 at the par-72, 7,253-yard Glen Abbey Golf Club.
Dustin Johnson shot 63 in rainy conditions on Saturday and also sits at 11 under after 54 holes.
Johnson didn't get news that Mahan, whose wife's due date was still a month away, was returning to Dallas until late in his round.
"It's one of those situations where you probably wouldn't expect him to have to leave. But sometimes that's just how it works," said Johnson, who played with Mahan through the first two rounds.
Mahan charged into the lead Friday with an 8-under 64 to improve on his 67 from the first round.
His start time had initially been set for 1:30 p.m. ET on Saturday before play was suspended for 80 minutes because of the threat of lightning in the area.
Mahan had been rescheduled to tee off at 2:50 p.m. but never made it to the course and instead rushed to the airport. With Mahan's withdrawal, Merrick played his round Saturday without a partner.
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