Rod Barajas hit a tying pinch-hit homer off Howell (6-4) with one out in the ninth. After walking three and with rookie Randy Ruiz up, Howell uncorked a wild pitch that bounced high and away from catcher Gregg Zaun, allowing Scutaro to score without a play.
It was Howell's seventh blown save.
Brandon League (2-5) worked one inning for the win.
It was a tough night to be a home plate umpire. Crew chief Jerry Crawford took a foul ball off his face mask and left after two innings while his replacement, Tom Hallion, was struck in the chest by a pitch from Rays lefty Scott Kazmir in the sixth.
Hallion was knocked backward when Travis Snider swung and missed at a two-strike pitch that seemed to cross up Rays catcher Zaun, slamming straight into Hallion. Trainers and medical staff rushed to Hallion's side and waved a cart onto the field. Hallion eventually stood up and walked off without assistance.
After a 21-minute delay, the game resumed with Hallion at third base. First base umpire Brian O'Nora moved behind the plate, and Scott Barry moved from third to first.
Toronto's comeback cost Kazmir his fifth win in six starts. Kazmir allowed one run and four hits in six innings. He walked one and struck out a season-high 10. It's the 17th time in his career Kazmir has fanned at least 10.
Rays reliever Russ Springer pitched the seventh, and Grant Balfour started the eighth but was replaced by Howell with two outs and runners at first and third. Howell got out of it by striking out Snider.
Seeking to win consecutive starts for the first time this season, Blue Jays rookie left-hander Marc Rzepczynski didn't allow a hit until Pat Burrell's two-out single in the sixth. Already struggling with a high pitch count, the rookie's shutout bid ended on the very next batter when Gabe Kapler homered into the left-field bullpen, his fifth, giving the Rays a 2-0 lead.
Rzepczynski allowed two runs and three hits in six innings. He walked a season-high five and struck out seven.
Toronto cut the deficit in half in the bottom of the sixth on an RBI double by Jose Bautista.
Making a rare start at third base, Toronto's John McDonald turned in the defensive play of the night in the second, leaping to his left to knock down a liner by Burrell, then throwing to first from his knees for the out.
Notes
One night after homering twice, Carlos Pena batted third for the first time this season. Rays manager Joe Maddon said he moved Pena up to give him protection by hitting ahead of Evan Longoria and Burrell. Pena went 0-for-2 and walked twice. … Maddon said OF Carl Crawford (sore lower back) is feeling better, adding there is "a solid chance" the speedy outfielder will play at Detroit on Friday. The Rays are off Thursday. … Rays Double-A LHP Darin Downs was released from the hospital Wednesday and is returning home, where he will continue to be under a doctor's care. Downs sustained a fractured skull when he was hit by a line drive Aug. 17. … The Blue Jays will send 1B David Cooper, 2B Brad Emaus, C Brian Jeroloman and OF Adam Loewen to the Arizona Fall League.