Baddeley added a second round 66 to an opening 68 to reach 10-under for the week, three behind leader Kevin Tway and part of a four way tie for sixth spot.
It was a blemish free round for the Victorian who is in need of some good results as he hovers precariously outside the top 125 on the FedEx Cup standings and in danger of losing playing privileges for 2019.
Three Australians will play the weekend at the Glen Abbey Golf Club after the cut was made at 4-under.
Cameron Percy is 8-under and T15 and Rod Pampling is 7-under and T23 while Matt Jones (3-under) and John Senden (3-over) failed to qualify for the final two rounds.
Baddeley made a fast start to his second round with four birdies in his first six holes but cooled with a run of nine straight pars.
Birdies at the 16th and 18th moved him to double figures and he will start the third round well in the mix.
Leader Kevin Tway, son of the 2003 Canadian Open winner Bob, was around in one stroke less than Baddeley and will take a one-shot lead into the third round at 13-under.
“I drove it well, made a few putts and made a bunch of birdies,” was his straightforward assessment after the round.
“I’ve played this course once before and it suits my eye. It’s generous off the tee which lets me hit driver a lot and that suits my game.”
Asked his strategy for the weekend he was equally blunt.
“Just try to keep going low and make as many birdies as possible,” he said.
“Pars are going to put you back so I’m going to keep playing aggressive.”
His nearest pursuers are Korea’s Whee Kim and another American, Keegan Bradley, with Ben An and Johnson Wagner a further shot back sharing fourth.
Overnight leader Robert Garrigus couldn’t maintain the momentum of his opening 63 and signed for an even par 72 to remain 9-under and T10.
World Number One Dustin Johnson is showing no signs of a hangover from his missed cut at last week’s Open Championship and added a 6-under 66 To his Thursday 68 to be just three off the pace and T6.
Rising Chilean star Joaquin Niemann also continues his remarkable run since turning professional in April, the 19-year-old alongside Johnson and Baddeley at 10-under after rounds of 67-67.
Niemann is on track for a fifth top 10 in 10 starts since joining the pay for play ranks and also received good new this week with an invitation to play the year’s final major, the PGA, next month.
Among some of the high-profile players to miss the cut were Masters champions Sergio Garcia and Bubba Watson as well as Matt Kuchar and local favourite Adam Hadwin.
RULES - IDENTIFYING AN UNMARKED GOLF BALL:
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