Napoli hit a shot into the fifth deck, the first at Rogers Centre in more than three years, as part of Boston's seven-run 11th inning and the Red Sox held on for a 11-7 win on Tuesday night.
Allen Craig also homered in the big inning, Dustin Pedroia homered and had four RBI and Boston won its second consecutive game following an eight-game losing streak.
"Standing at home plate, it's hard to imagine hitting a ball that far, but he did," Craig said.
Toronto fell to 6-16 in August and, at 66-66, dropped to .500 for the first time since May 15. The Blue Jays have played four straight extra-inning games, losing three.
"It's tough," Toronto's Casey Janssen said. "We lost another tough game in extra innings."
Mookie Betts singled off Janssen (3-2) to begin the 11th and was called out at second on Christian Vazquez's sacrifice, with the call overturned after a challenge by Red Sox manager John Farrell. Janssen was charged with an error when he bobbled Brock Holt's bunt, loading the bases for Pedroia, who singled through the drawn-in infield to score a pair.
Sergio Santos came on and struck out Yoenis Cespedes before Napoli, who was hit on the helmet by a pitch earlier in the game, crushed a towering three-run homer into the fifth deck. It's the 17th upper-deck homer in the 25-year history of Rogers Centre, and the seventh by an opponent.
"I was just trying to hit the ball hard somewhere, trying to get a single with a runner in scoring position," Napoli said. "I guess it's pretty cool."
Daniel Nava doubled before Craig homered, his first with Boston.
Blue Jays manager John Gibbons, who'd already used all his available relievers, responded by calling designated hitter Steve Tolleson out of the dugout to take the mound. Tolleson struck out Will Middlebrooks and got Betts to fly out to the warning track.
Napoli was hit on the brim of the helmet by a wayward knuckleball from R.A. Dickey in the fifth, knocking it off his head. His face showing concern, Dickey held his hands up in apology.
"It doesn't feel good," Napoli said of being beaned by a knuckler, insisting he had no lingering effects.
Junichi Tazawa (3-3) worked one inning for the win. Heath Hembree allowed three runs in the 11th, but Boston held on.
Pedroia homered off Dickey in the first and Middlebrooks made it 3-0 with a two-out double, but Toronto tied with single runs in the third, fourth and fifth.
The Red Sox reclaimed the lead against Dustin McGowan in the seventh on an RBI single by Cespedes, but Jose Bautista led off the bottom half with a tying homer off Alex Wilson, snapping an 0-for-17 slump.
Bautista is the third player in Blue Jays history to record five consecutive seasons with 25 or more home runs. The others are Joe Carter, who did it six times between 1991-96, and Carlos Delgado, who did it nine times from 1996-04.
Major League Baseball denied a protest filed by Tampa Bay manager Joe Maddon in Saturday's game, which Toronto won 5-4. Maddon protested after crew chief Bob Davidson allowed Gibbons to challenge a pickoff play at first base after pitcher Mark Buehrle had returned to the rubber and batter Yunel Escobar had returned to the box. "We might have been winless for the week if they'd nailed that thing," a relieved Gibbons said.
Red Sox: DH David Ortiz (right foot) sat out his second straight game. Ortiz left Sunday's game against Seattle in the sixth, two innings after fouling a ball off his foot. Manager John Farrell said Ortiz, who skipped batting practice, could play Wednesday.
Blue Jays: OF Colby Rasmus (illness) was scratched from the lineup shortly before first pitch and replaced by Kevin Pillar, who was recalled from Triple-A Buffalo earlier Tuesday. Toronto designated OF Nolan Reimold for assignment to make room for Pillar.
Red Sox RH Joe Kelly (0-1) takes on Blue Jays RH Marcus Stroman (7-5) in Wednesday's series finale. Stroman has lost his last three decisions and allowed a career-high 10 hits in his previous start, Aug. 22 against Tampa Bay.
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