Judge had one walk but ended up none-for-three with two strikeouts and a fly out to medium center as the wait draws on to pull level with Roger Maris' franchise and American League (AL) record of 61 home runs in a single season.
The Yankees outfielder was left frustrated when he tried to hold his swing on a wide 2-2 fastball but umpire Chris Conroy signaled a third strike.
"Even for a guy that hit 60 home runs, he still doesn't hit them every day," Yankees coach Aaron Boone said. "A lot of things got to line up to go deep, even for the best of the best. So as long as he continues to take good at-bats and make good swing decisions, it'll happen sooner rather than later."
Judge's showing meant his batting average dropped to .314, with Boston's Xander Bogaerts going two-for-four to move ahead of him at .315, denting the Yankee's triple crown hopes.
Anthony Rizzo's seventh-inning two-run blast earned the Yankees the win in front of a sell-out crowd after scores were locked at 5-5.
Manoah helps Blue Jays claim key win
Alex Manoah led the way as the Toronto Blue Jays regained the top AL Wild Card spot with a 3-1 victory over the Tampa Bay Rays.
Manoah sent down seven shutout innings with eight strikeouts – including his 300th career K - allowing only four hits with two walks.
Whit Merrifield hit a seventh-inning three-run blast to open up a three-run lead, capping a strong week after two homers against the Rays on Thursday.
The win means the Blue Jays (85-67) lead the Rays (84-68) by one game for the first AL Wild Card spot. The Seattle Mariners (83-68) are next.
Padres make ground in NL Wild Card hunt
Darvish finished with eight strikeouts across six innings, allowing only five hits and two runs, but the Padres pulled clear with a six-run seventh inning.
Jake Cronenworth and Ha-Seong Kim both had two-run singles amid the seventh inning where they turned a tight game into a rout. The Padres move to 84-68, ahead of the Philadelphia Phillies (83-68) in the NL Wild Card race.