Mahan was 13 under after two rounds when he got a call saying wife Kandi had gone into labor with their first child. The American rushed to the airport for a flight to Texas.
Snedeker had a 9-under 63 at Glen Abbey to take the lead after the rain-delayed third round. There were scattered showers and an 80-minute delay because of lightning.
Sweden's David Lingmerth was a stroke back after a 65, and Matt Kuchar and Jason Bohn were 12 under. Kuchar had a 64, and Bohn shot 66.
Dustin Johnson also shot 63 to share 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 playoff alongside a non-scoring marker.
Leading third-round scores on Saturday in the US PGA Tour $5.6 million Canadian Open (USA unless noted, a-denotes amateur, par-72)
202 - Brandt Snedeker 70-69-63
203 - David Lingmerth (SWE) 67-71-65
204 - Matt Kuchar 66-74-64, Jason Bohn 70-68-66
205 - Dustin Johnson 75-67-63, Kyle Stanley 68-71-66, Greg Owen (ENG) 70-68-67, Charley Hoffman 69-69-67, John Merrick 71-62-72
206 - Mark Wilson 70-69-67, Roberto Castro 69-70-67, James Hahn 69-68-69, Patrick Reed 68-68-70
207 - Trevor Immelman (RSA) 68-73-66, Fabian Gomez (ARG) 72-68-67, William McGirt 71-69-67, Jeff Maggert 72-67-68, Alistair Presnell (AUS) 72-67-68, Jim Furyk 72-67-68, Bubba Watson 68-67-72
208 - Vijay Singh (FIJ) 69-73-66, Greg Chalmers (AUS) 73-68-67, Chris Kirk 68-69-71
209 - Charl Schwartzel (RSA) 73-70-66, Chad Campbell 71-72-66, Matt Every 71-71-67, Chez Reavie 68-73-68, Jason Kokrak 72-68-69, Hideki Matsuyama (JPN) 69-69-71 209, James Driscoll 69-69-71, Aaron Baddeley (AUS) 68-68-73