Snedeker had eight birdies and an eagle in his 10-under round but was overtaken for the halfway lead by Matt Kuchar and Scott Brown, who both carded seven-under 63s to top the leaderboard at 12-under 128.
"I drove the ball fantastic," said Snedeker, whose sparkling round came nine months after he became just the ninth golfer in US PGA Tour history to fire a 59. "I think I missed two fairways today, you do that around here you set yourself up for success.
"Made a couple of putts early to kind of get the momentum going. I just gave myself a lot of opportunities."
Snedeker really shone on the greens, rolling in a total of 136 feet of putts on the course near Toronto, falling just shy of joining Jim Furyk as the only players to break 60 twice on the PGA Tour.
The affable 38-year-old from Tennessee opened with a birdie at the par-four 10th, and added birdies at 12, 16 and 17.
Playing alongside four-time major winner Brooks Koepka and big-hitting Justin Thomas, Snedeker, kept things rolling coming in, his birdie at the second followed by a 20-footer for eagle at the par-five fourth. He drained another long one -- 21 feet -- for birdie at the fifth, watched a 14-footer drop at the sixth and capped his round with a six-footer at the ninth.
"When I get hot the hole is like a beach ball to me," Snedeker said of his performance on the greens. "Today I felt like that.
Although he couldn't claim a second 59, Snedeker became the fourth player to card multiple rounds of 60 or lower. He now has a 59 a 60 and a 61 on his PGA Tour resume.
"You don't get these days very often on tour," he added. "More often you're getting beat up, so when you have these days you've got to take advantage of them."
Snedeker shared third place with Nick Taylor, who carded a 65 for 129 and led a group of four Canadians within four shots of the lead trying to post the first home win in the tournament since 1954.
Leading second-round scores on Friday in the US PGA Tour Canadian Open at Hamilton Golf and Country Club in Toronto (par-70):
128 - Scott Brown 65-63, Matt Kuchar 65-63
129 - Brandt Snedeker 69-60, Nick Taylor (CAN) 64-65
130 - Webb Simpson 66-64
131 - Adam Hadwin (CAN) 65-66
132 - Mackenzie Hughes (CAN) 66-66, Henrik Stenson (SWE) 66-66, Graeme McDowell (NIR) 65-67, Ben Silverman (CAN) 71-61, Shane Lowry (IRL) 64-68, Im Sung-jae (KOR) 64-68
133 - Sepp Straka (AUS) 68-65, Rory McIlroy (NIR) 67-66, Jose de Jesus Rodriguez (MEX) 67-66
134 - Peter Malnati 66-68, Hank Lebioda 67-67, Ben Crane 69-65, Adam Schenk 66-68, Jonas Blixt (SWE) 67-67, Danny Willett (ENG) 66-68, Brian Harman 69-65, Keegan Bradley 63-71, Erik van Rooyen (RSA) 64-70
But it was Kuchar and Brown leading the way into the weekend in the last tune-up event before next week's US Open.
Brown teed off on 10 and eagled the par-five 17th before reeling off five straight birdies from the second through the sixth.
Kuchar had eight birdies, including three in a row from the third through fifth and another three straight to end his round.