TORONTO -- The Blue Jays had a sweep in mind, looking for their fifth straight win for the first time this season, but the Mets had other plans.
Henderson Alvarez was roughed up from the start, while the bats came up just short during a pair of late-inning rallies, as the Blue Jays lost, 6-5, at Rogers Centre in front of 41,867 fans, the largest crowd since Opening Day.
On Friday, the Blue Jays used a season-high 14 runs and on Saturday got a gem from right-hander Brandon Morrow to put them ready to break out the brooms. But Sunday, the Mets jumped ahead with a three-run first inning and added on, which was needed as the Blue Jays made things interesting late.
"I thought the first couple of innings, [Alvarez] was so strong coming out of the bullpen, he was almost throwing through his sink," Blue Jays manager John Farrell said. "Some fastballs straight down, they get up in the zone and they bunch some hits together from the three runs in the first.
"I think today was probably the one day that he came out so strong, his normal sinker didn't have quite the depth. ... Couple of pitches up in the strike zone early on contributed to some of those runs."
Alvarez, who had a string of five consecutive quality starts snapped, lost his second straight decision and turned in his worst performance since an April 19 loss to the Rays. It was the time he failed to pitch at least six innings since Aug. 15, 2011, a span of 16 straight starts.
The 22-year-old allowed three runs in the first inning on three extra-base hits, while the Mets sent seven men to the plate.
After the first two batters reached base, David Wright, who was sick and missed Saturday's contest, drove in two with a double to center. A few batters later, it was Kirk Nieuwenhuis' turn, as he cashed in Wright with a double.
Alvarez's struggles continued into the second inning as Mike Baxter, who doubled in the first, drove home Ronny Cedeno with a triple to right field to increase the Mets' lead to 4-0.
The Blue Jays got one back for Alvarez in the bottom half of the frame on a first-pitch single by rookie Yan Gomes to bring home Ben Francisco, who led off the inning with a walk. Then in the third, Jose Bautista hit a solo homer, his sixth in his last 10 games, that just barely scraped the fence in left.
But Alvarez ran into more problems in the fifth, as the Mets added two more to make it a 6-3 ballgame and end his day. All six runs surrendered by Alvarez were earned, matching his career high, while he walked a pair and struck out three. He has allowed 19 hits in his past two starts.
Alvarez admitted that he had trouble locating his two- and four-seam fastballs, but he was trying to stay positive.
"There are always good days and bad days -- I feel like I didn't have a good day today," Alvarez said through interpreter Luis Rivera. "Things happen when you pitch, but I will learn from this start."
Baxter, who finished the game 3-for-4, and was a key part of the Mets' early damage off Alvarez, was still impressed with his stuff.
"A heavy sinker," Baxter said. "In my later at-bats, I think he located it better. He threw me a couple pitches down in the zone that I know if he was there all game, he'd be extremely effective. To me, there were a couple pitches up that I was able to get. But when he threw the pitch where he wanted it, it was heavy, it was hard and there was great movement on it."
Once Alvarez left the game, Toronto's bats came to life.
First, it was Bautista who helped Toronto chip away with an RBI single up the middle in the seventh that chased Mets starter Dillon Gee from the game.
The following inning, the Blue Jays had their way with Mets reliever Bobby Parnell. J.P. Arencibia led off with a double to left, his second hit of the game, and was promptly cashed in by Eric Thames, who hit a 1-1 slider down the line in right to make it 6-4.
Two batters later, Colby Rasmus, who sat in place of Rajai Davis the first two games of the series, busted out of an 0-for-20 skid with a base hit to center that drove in Thames, pulling Toronto within one.
The Blue Jays entered the ninth trailing, 6-5, and Toronto fans welcomed familiar face Frank Francisco with a chorus of boos as he came out of the bullpen door and made his way to the mound to close out the game.
Yunel Escobar and Bautista reached base to start the inning, putting runners on first and second with none out for Edwin Encarnacion.
Francisco got Encarnacion to strike out, then followed with two more K's on Arencibia and Thames to thwart the rally and end the game.
"Those guys at the back end of their bullpen make their money for a reason," said Arencibia, who went 2-for-5. "Frankie at the end of the game punched out the side after the first two batters getting on -- he's got good stuff.
"Sometimes, you have to give credit to the others."
Toronto finished its homestand with a 4-3 record.
After getting swept in a mini two-game set to the Rays, the Blue Jays did the same to the Yankees and then took two out of three from the Mets.
Farrell was pleased with the effort his club showed after the Rays series.
"I thought we responded in the Yankees series," Farrell said. "Guys are playing extremely focused. The conclusion of today's game, the way we continued to chip away and put together some opportunities for us. This team is clearly focused."
Chris Toman is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.