SAN FRANCISCO -- In the end, an early exit by Anthony DeSclafani and a ninth-inning blip from closer Jake McGee proved too much to overcome for the Giants, who fell short of a three-game sweep in a 6-2 loss to the Mets in 12 innings on Wednesday afternoon at Oracle Park.

• Box score

Kevin Pillar, who was non-tendered by the Giants following the 2019 season, delivered the knockout punch, slugging a three-run homer off Tyler Chatwood to snap a 2-2 tie in the 12th. Chance Sisco added an RBI double to cap the Mets’ four-run rally off Chatwood, who allowed five runs (three earned) on five hits over two innings in his San Francisco debut.

“This loss sucked because we kind of put it all out there and gave everything we had,” manager Gabe Kapler said. “We used every piece of our roster and came up empty.”

DeSclafani departed after recording only four outs due to right ankle discomfort, but the Giants’ bullpen nearly picked him up with a heroic effort. José Álvarez, Zack Littell, Jarlín García, Dominic Leone and Tyler Rogers delivered 6 2/3 scoreless innings to turn a one-run lead over to McGee in the ninth.

Still, the Mets rallied to tie the game at 1-1. Pete Alonso was hit by a pitch, advanced to third on Conforto’s single and scored on J.D. Davis’ sacrifice fly. McGee then received a huge assist from shortstop Brandon Crawford, who made a terrific diving play up the middle to snag Dominic Smith’s grounder. Crawford flipped to Kris Bryant to record the forceout at second base, preventing the Mets from adding on and helping send the game to extras.

Tony Watson, pitching for the third consecutive day, worked a scoreless 10th with the help of LaMonte Wade Jr., who robbed Pillar of extra bases with a leaping catch at the left-field wall.

The Giants had a chance to end it after putting runners on second and third with two outs in the bottom of the 10th, but Mets closer Edwin Díaz coaxed an inning-ending flyout from Wade to keep the game tied. Wade opened the scoring with an RBI double in the third, but the Giants’ No. 3-7 hitters finished 0-for-22 with 10 strikeouts.

Down to their last reliever, the Giants sent Chatwood to the mound in the 11th, but he surrendered a double to Michael Conforto that scored automatic runner Jeff McNeil and put the Mets ahead, 2-1.

“That was my first time with that runner on second,” said Chatwood, who joined the Giants on a Minor League deal on Aug. 5. “It’s different, but I’ve got to go out there and do my job and get outs.”

The Giants pulled even on Tommy La Stella’s RBI single off Jeurys Familia in the bottom of the 11th, but Chatwood again couldn’t keep the Mets at bay in his second inning. Jonathan Villar nearly opened the inning with an RBI double, but his shot down the left-field line was ruled foul following a replay review. Chatwood ended up striking out Villar, but he then allowed a single to Patrick Mazeika, setting up Pillar’s three-run blast to left field.

“Chatwood, in that situation, did everything that we could ask him to do,” Kapler said. “Obviously, he’d like to have that sinker back that he threw to Pillar that ran middle-in, or into a spot where Pillar could get it in the air. But for the most part, what we’re looking for from Chatwood is to depend on his stuff. And his stuff was pretty good. The ball was coming out good. We saw some swings and misses. But ideally, we’d like to find a softer landing spot for any of our new pitchers.”

The afternoon began on a suboptimal note for the Giants, as the 31-year-old DeSclafani began to feel irritation on the outside of his right ankle after striking out Davis to end the first inning. The pain increased in the second, when he ran to cover first on Smith’s groundout to start the inning. DeSclafani subsequently issued a five-pitch walk to Villar, with his final pitch clocking in at 90.7 mph, several ticks below the 94.3 mph he has averaged on his four-seam fastball this year.

Kapler and head athletic trainer Dave Groeschner came out to check on DeSclafani, who ended up walking off the field after allowing one hit in 1 1/3 innings.

“When I would go to throw a pitch and push off, I was getting pain,” DeSclafani said. “I think it was kind of smart to get out of there before you hurt something else.”

It was DeSclafani’s shortest start of the year and only his second since returning from the injured list last week. He missed one start due to right shoulder fatigue, but he came back to work five innings of two-run ball against the Rockies on Friday.

DeSclafani will undergo an MRI exam on Thursday, though he said he was feeling better after the game and hopes to stay day to day. Still, DeSclafani’s injury is the latest rotation concern for the Giants, who already have veteran right-hander Johnny Cueto on the IL with a right flexor strain.

With a 7-2 homestand against the D-backs, Rockies and Mets in the books, the Giants will take a much-needed off-day on Thursday before heading across the bay to kick off a three-game series against the A’s on Friday.