The Mets closer gave up a walk and a single to start the bottom of a nervous ninth inning but regained his composure to strike out the next three Blue Jays batters as New York downed Toronto 6-5 to salvage the finale of a three-game interleague series.
"I'm deaf," Francisco said of the jeers after recording his 10th save of the season. "I don't hear anything."
Francisco walked Yunel Escobar and gave up a single to Jose Bautista before striking out Edwin Encarnacion, J.P. Arencibia and Eric Thames.
On the cold reception at Rogers Centre, Francisco, who served as the Blue Jays' closer for parts of last season when he had 17 saves against four blown opportunities, dead-panned that Toronto fans "love me and I left."
The Blue Jays, meanwhile, ended a 4-3 homestand on a losing note as the club heads out on a six-game roadtrip to Tampa Bay and Texas.
"Those guys at the back end of the bullpen make their money for a reason. (Francisco) punched out the side after the first two batter getting on ... he's got good stuff," Arencibia said. "He's throwing 98 (miles per hour) down and away — it's not easy."
New York's Mike Baxter finished a home run short of the cycle and a had career-high three hits, while David Wright boosted his major-league leading average to .412 as the Mets took advantage of Toronto starter Henderson Alvarez's shaky outing.
The right-hander gave up six earned runs, including three in the first, on nine hits and two walks in front of a crowd of 41,867.
"I think today was the one day that (Alvarez) came out so strong that his normal sinker didn't have quite the depth (it needs)," Blue Jays manager John Farrell said. "Just a couple pitches up in the strike zone early."
Alvarez, who finished with three strikeouts on the afternoon and came in having given up just six earned runs combined in his previous five starts, agreed with Farrell's assessment.
"Everything got a little complicated," Alvarez said through a Spanish interpreter. "You always have good days and bad days. I didn't have a good day today but I'll learn from this start."
Baxter had two cracks at completing the cycle but preferred to stay focused on what was working.
"It crossed my mind, but I didn't really want to get away from what I've been doing," said Baxter, who finished 3-for-4 with an RBI and two runs scored. "I just want to try and keep the same approach, I don't want to start messing with it."
Dillon Gee gave up three earned runs on five hits to go along with six strikeouts and four walks over 6 2-3 innings for New York, which improved to 15-6 all-time against Toronto. Wright was 2-for-4 with a walk and two RBIs.
"This is a crazy game. I was all over the place today," said Gee, who picked up his first win in four starts. "Last game I felt great and I gave up seven runs. Today I felt terrible, like I couldn't throw a strike, and I give up three. I don't know. It's a crazy game. "
Bautista hit his 11th home run of the season and finished with two RBIs for Toronto, which saw its four-game winning streak snapped.
Trailing 6-3 in the eighth, Arencibia and Thames hit back-to-back doubles off Mets reliever Bobby Parnell to cut the lead to two. Colby Rasmus then snapped an 0-for-20 slump with a single up the middle to score Thames from second.
But Parnell struck out Yan Gomes and Tim Byrdak came out of the Mets bullpen to get Kelly Johnson on a flyout.
The Blue Jays chipped away at the New York lead in the seventh after Gee hit Gomes to lead off the inning. The Toronto third baseman later scored on a two-out single to centre by Bautista, but Parnell replaced Gee and induced a forceout from Encarnacion to end the threat.
After Luis Perez tossed two scoreless innings of relief for the Blue Jays, Carlos Villenueva came in for the eighth and loaded the bases but got Wright to strike out with two outs.
"I thought today was another example of our competitiveness, our ability to reach down when needed," Farrell said. "We felt like we set it up in the ninth down a run, get the first two guys on in the middle of the order where we've been able to do some damage of late.
"Certainly not the way we envisioned things turning out after the first two guys get on in the ninth."
The Mets got to Alvarez (3-4) in the top of the first. After leadoff man Andres Torres walked and Baxter doubled to put runners on second and third, Wright doubled to score two.
After a groundout and a strikeout, Kirk Nieuwenhuis hit a sinking liner to centre that was initially caught by a diving Rasmus, but the Toronto centre-fielder saw the ball pop out his glove as New York scored its third run of the inning.
Alvarez got into more trouble in the second when Ronny Cedeno scored from third on a Baxter triple.
The Jays (23-19) got one back in the second. After back-to-back walks to Francisco and Rasmus, Gomes singled to left to score one. Gee (3-3) got out of the jam with consecutive forceouts off grounders by Johnson and Escobar.
Bautista then cut the New York lead to 4-2 in the third with a solo home run to left.
But the Mets (22-19) restored their three-run lead in the fifth when Baxter and Wright singled. After Lucas Duda hit into a forceout at second, Daniel Murphy singled to centre to score Baxter from third.
Alvarez then walked Nieuwenhuis to load the bases and a forceout at second on an Ike Davis grounder scored Duda to make it 6-2.
Notes: Ben Francisco was replaced in right field by Rajai Davis in the sixth inning as a precaution due to tightness in his left hamstring. ... Blue Jays third baseman Brett Lawrie sat out the final game of his four-game suspension for throwing his batting helmet that bounced up and hit umpire Bill Miller on Tuesday night. ... The Blue Jays fell to 125-143 all-time in interleague play, while the Mets improved to 128-122 against American League opponents. ... The Blue Jays resume interleague play with a series in Atlanta beginning June 8. ... Farrell refused to comment prior to the game on reports that first baseman Adam Lind was placed on outright waivers when he was sent to triple-A Las Vegas earlier this week. ... Farrell said outfielder Travis Snider took himself out of a triple-A game on Wednesday after feeling some discomfort in his right wrist while swinging a bat. ... The Mets placed starter Miguel Batista on the 15-day disabled list with a lower-back strain and recalled fellow right-hander Chris Schwinden from triple-A Buffalo.