HOUSTON—Francisco Rodriguez's alleged assault of his girlfriend's father last week has had some very real—and very damaging—results for the Mets. Mr. Rodriguez, the team's closer, sustained a torn ligament in the thumb of his pitching hand during the altercation, a team spokesman said Monday, and it is unlikely he will pitch again this season.

Mr. Rodriguez, who leads the Mets with 25 saves, did not travel with the team here for its four-game series against the Astros.

He was examined Monday at the Hospital for Special Surgery in Manhattan. A magnetic resonance imaging test revealed the tear, and team doctors have recommended that Mr. Rodriguez undergo surgery to repair it. The date of the surgery is yet to be determined.

After serving a two-day suspension following the incident, which allegedly took place in the Mets' family lounge at Citi Field on Wednesday, Mr. Rodriguez pitched a scoreless inning Saturday. He then complained of discomfort in his right hand, according to the team spokesman and manager Jerry Manuel.

Josh Thole, who caught the inning that Mr. Rodriguez pitched on Saturday, said he noticed "there was something going on" with Mr. Rodriguez's pitches.

"He wasn't throwing the types of strikes he normally does," Mr. Thole said.

When asked whether the team would punish Mr. Rodriguez or attempt to void his contract—Mr. Rodriguez signed a three-year, $37-million deal with the Mets in 2009—the spokesman said he was not in a position to answer the question.

General manager Omar Minaya and assistant general manager John Ricco did not make the trip here.

With a midnight deadline looming, Mr. Minaya and Mr. Ricco were still negotiating a contract with first-round draft pick Matt Harvey and Mr. Harvey's agent, Scott Boras.

Agent Paul Kinzer, who represents Mr. Rodriguez, did not return a phone call to his office.

Despite the team's decision to suspend Mr. Rodriguez last week—the two days without pay cost Mr. Rodriguez more than $125,000—Mr. Manuel suggested there were mitigating circumstances surrounding the incident that made him sympathetic toward Mr. Rodriguez.

"When you have some of the information, not all of the information, and you can pass judgment on the little information you have, you don't condone it, but you can see why," Mr. Manuel said. "I think that has to be taken into account with your frustrations."

Mr. Manuel would not elaborate on what information or details he knew about the situation because "it was a legal-type thing. It would only be fair to the people involved to stay away from that."

As for who would replace Mr. Rodriguez as the Mets' closer, Mr. Manuel named five of the six relievers who are on the team's active roster.

The only one he did not mention was Oliver Perez.

Write to Mike Sielski at mike.sielski@wsj.com