Brett Baty’s rookie season is in all likelihood over.

The team’s No. 2 prospect, given a shot at the major league level in the wake up Luis Guillorme’s groin injury, suffered a UCL tear in his right thumb that will require surgery, the Mets announced before Wednesday night’s 2-1 win over the Dodgers at Citi Field.

Baty hurt his thumb Sunday against the Rockies while diving for a foul ball. The typical recovery time, the Mets said, is five weeks, which would come after the regular season is over. Baty hit .184/.244/.342 in 11 games with a .586 OPS. He homered in his first at-bat against the Braves.

Fortunately for the Mets, Eduardo Escobar recently came off the 10-day injured list and Luis Guillorme is close to starting a minor league rehabilitation assignment. Guillorme, out since Aug. 14 with a left groin strain, has been swinging and taking ground balls the past few days. He has yet to run full speed. That is the last hurdle before he can appear in minor league games. Guillorme and Escobar platooned at third base before Guillorme’s injury.

“It’s definitely feeling better,” Guillorme said. “It’s a matter of when I’m ready. …. We’re just checking all the boxes, making sure everything’s fine. There’s no point in rushing something for me to come back.”

That was before the extent of Baty’s injury was known. Outfielder Terrance Gore replaced Baty on the active roster, leaving the Mets without a backup infielder for the time being.

After the game, manager Buck Showalter said there is an “outside possibility” Baty could return at some point this year.

Tylor Megill is closing in on his long-awaited return and is hoping to be a key cog in the Mets’ bullpen when he gets to that point.

The right-hander (shoulder strain) told The Post he will start a rehabilitation assignment with Double-A Binghamton on Thursday, and the plan is for him to make five outings before rejoining the Mets.

Megill will throw one inning in his first few appearances and progress to two. His second outing is scheduled for Sunday. Megill was a reliever in college, so he has experience in this new role.

“I’m all for it,” he said. “If I can help out in the bullpen, that’s what I will do. … Going out filling up the strike zone is the biggest thing.”

Megill threw a 25-pitch live batting practice session on Monday. He last appeared in a game on June 16. Megill started the year exceptionally well, pitching to a 1.93 ERA in five April starts. But injuries to his right biceps and shoulder have sidelined him for much of the past four months.

“I feel really good,” he said.

In addition to Megill, manager Buck Showalter said that Drew Smith (right lat strain) is also close to pitching in minor league games, though they haven’t settled on a specific day yet.

The Mets appear to be considering a six-man rotation for their starting pitchers the next time through. Showalter said Carlos Carrasco (left oblique strain) could return to the rotation this weekend and David Peterson may start as well, potentially giving Taijuan Walker and Jacob deGrom an extra day of rest. The only certainty at the moment is Chris Bassitt starting Thursday’s series finale against the Dodgers.

With the rosters expanding by two players on Thursday, Showalter said catcher Michael Perez is an option for a call-up. The 30-year-old veteran performed well in place of Tomas Nido before being sent to Triple-A Syracuse.

Showalter made it seem unlikely prospect Mark Vientos would get the call, though that was before Baty needed surgery. The issue for Vientos is the presence of trade-deadline addition Darin Ruf as the right-handed platoon at DH.

“We’re hoping he finishes up strong down there and completes a pretty good season,” Showalter said.

Vientos, the Mets’ seventh-ranked prospect according to MLB Pipeline, has 23 home runs, 71 RBIs and a .903 OPS in 346 at-bats for Syracuse.