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MIAMI — It was a much-needed win for the San Francisco Giants, but it came at a great cost.

Pablo Sandoval’s tie-breaking two-run single in the 16th inning lifted the Giants past the Miami Marlins 6-3 on Thursday, but the Giants also lost third baseman Evan Longoria to a broken left hand after he was hit by a pitch.

“A great win, but a tough loss,” Giants manager Bruce Bochy said.

Longoria sustained a fracture to his fifth metacarpal, which could require surgery. A decision is expected in the next couple of days.

“Obviously the goal is to decide something as soon as possible and then get going in the right direction, whether that’s put a cast on it and just let it sit or have some sort of surgery and go that route,” Longoria said.

Longoria initially stayed in the game to run after he was hit in the fourth inning, but came out in between innings.

“It wasn’t my legs,” Longoria said. “I just hate coming out of the game right away. I’ve always thought it looked bad. I knew right away that it didn’t feel right, but I just figured I could run and in the meanwhile let (Alen Hanson) get loose and come into the game.”

Longoria is hitting .246 with 10 home runs and 34 RBIs in 67 games.

“It’s a tough loss,” Sandoval said. “I don’t know how many days he’s going to be out, but we’re going to miss the guy. He’s a great hitter, great defensive player, and a great teammate. I hope he recovers well and comes back to help us get to the postseason.”

Andrew McCutchen hit a two-run homer to continue his torrid month and Mac Williamson also homered for the Giants, who salvaged the final game of a four-game series and beat the Marlins for only the second time in the past 10 meetings.

“It was a great win to head home on after a tough series,” Bochy said. “I’m looking forward to getting out of Miami, trust me.”

Giants’ starter Dereck Rodriguez pitched 6⅔ innings, allowing two runs with his father and former Marlins’ World Series championship catcher Pudge Rodriguez sitting behind home plate. Ty Blach (4-5) also pitched 6⅔ innings for the Giants without allowing a run. He gave up seven hits, walked two, and struck out three.

“Two quality starts in one game. I’ll take it,” Rodriguez said.

Sam Dyson came on for Blach to get the final out with two runners on for his first save of the season.

McCutchen started the 16th with a single, Brandon Crawford walked and Alen Hanson singled to load the bases of Elieser Hernandez (0-4). Sandoval’s single to center made it 5-3, and Gorkys Hernandez added a sacrifice fly later in the inning. The runs were the first for the Giants since the second.

“I just tried to calm down — everyone was tired — and tried not to do too much,” Sandoval said.

Miami had two runners on in the bottom of the 16th for Bryan Holaday, who flew out to end the game.

“Epic game,” Bochy said.

It was the longest game of the season for the Giants and the second-longest for the Marlins, who went 17 innings in a 2-1 win over the Cubs on March 30.

Both teams had opportunities in extra innings after the Marlins tied the game in the bottom of the ninth off Hunter Strickland on a sacrifice fly by Lewis Brinson. Second baseman Joe Panik was unable to hold onto a pop up near the foul line, allowing the lead-off runner to reach.

It was the eighth time in the series the Marlins came back to tie the game.

“It was one of those series where you kind of play back and forth,” Marlins manager Don Mattingly said. “Close games. Good for a lot of situations.”

The Giants looked to take the lead in the 11th on a double by Hanson, but Crawford was thrown out at the plate.

Miami threatened in the 13th when Bochy ordered an intentional walk to Starlin Castro load the bases with two outs and Hernandez due to bat because the Marlins were out of position players. Hernandez bounced to Blach.

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