Mahan was 13-under after two rounds when he got a call before he was scheduled to tee off Saturday saying wife Kandi had gone into labor.
He rushed to the airport for a flight to Texas.
“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.”
Snedeker had 9-under 63 at Glen Abbey to take the lead after the rain-delayed third round. He won the Pebble Beach National Pro-Am in February for his fifth PGA Tour victory.
“I know how to handle it and I know what to expect tomorrow especially on a golf course like this,” Snedeker said. “I’m not too concerned about my number right now. I know what I have to do tomorrow.”
The 2012 FedExCup champion had nine birdies in a bogey-free round.
“I knew I had a chance if I could keep the momentum going after the first six holes and I could really ride it out and do something special today,” Snedeker said.
There were scattered showers and an 80-minute delay because of lightning.
David Lingmerth is a stroke back after 65, and former Georgia Tech standout Matt Kuchar and Jason Bohn are 12-under. Kuchar had 64, and Bohn shot 66.
Dustin Johnson also shot 63, good for a tie for fifth at 11-under with John Merrick (72), Greg Owen (67), Charley Hoffman (67) and Kyle Stanley (66).
Merrick, two strokes behind Mahan on Friday after a matching the course record with a second-round 62, played alone in the third round after Mahan withdrew. Merrick declined to play alongside a nonscoring marker.
David Hearn was the top Canadian, shooting 68 to reach 5-under. Former Masters Tournament champion Mike Weir is 3-under after 73.