The Mets’ hope of pitching their two best starters against the Yankees was dashed Friday when Noah Syndergaard’s index finger flared up following a game of catch.

Syndergaard, who was scheduled to come off the disabled list Sunday and pitch in the Subway Series finale, has been scratched from his start and will be replaced in the rotation by Seth Lugo, according to manager Mickey Callaway.

“It’s something we knew could happen, that is why we threw [Syndergaard] in a simulated game instead of an actual game [Tuesday],” Callaway said. “So I think we did the right thing there, but we would love for him to pitch Sunday, but that’s not the case. Seth Lugo is going to step up and do a good job in his spot.”

Syndergaard was placed on the DL following his May 25 start in Milwaukee with a strained ligament in his index finger. He threw 25 pitches in his simulated game Tuesday.

The new best-case scenario for the Mets is Syndergaard throwing a bullpen session or simulated game within the next few days and then perhaps rejoining the rotation next weekend at Arizona.

Lugo started against the Cubs last week and then returned to the bullpen for three shutout innings in relief against the Orioles on Tuesday. In his start against the Cubs, the right-hander pitched four scoreless innings.

Lugo is 1-1 with a 2.04 ERA overall this season. Lugo’s lone career appearance against the Yankees came in 2016, when he allowed one run in one inning of relief against them.