Joe Torre, MLB's executive vice-president for baseball operations, told The Associated Press in a phone interview the decision was made to keep policy consistent throughout baseball.
"Certainly it's not a lack of respect," Torre said. "We just felt all the major leagues are honouring the same way with the American flag on the uniform and the cap. This is a unanimity thing."
The Mets wanted to wear caps honouring police, firefighters and other first responders like the ones they wore on Sept. 21, 2001, in the first professional sporting event in New York after the World Trade Center collapsed 10 days earlier. They spoke with Torre on several occasions over the course of the last month.
"They certainly understood and respected," baseball's decision, Torre said. "I certainly understood what they wanted to do in regards to wearing the hats. I used my history with the fact that we were in the World Series 10 years ago."
During the 2001 World Series, the Yankees wore caps with emergency service logos during a pregame ceremony, but wore their blue hats with a white interlocking "NY" for the games.
Torre also said there was recent precedence for the policy. The Washington Nationals wanted to wear caps honouring the Navy SEALs that were killed in Afghanistan in early August and the team was allowed to wear them before the game.
The Mets said in a statement Sunday they followed the guidelines set in a league-wide memo issued by MLB for games played on Sept 11.
Some Mets wore caps, such as "NYPD" and "FDNY," during batting practice. Player representative Josh Thole said he and his teammates were contemplating wearing those caps during the game.
"I think it will be a nice gesture," Thole said. "What are they going to do, fine us?"
Several minutes later he returned and said the caps were a "no-go" because he was told MLB was adamant.
"If we got a vote in, I think we'd want to wear the hats," David Wright said, "but at the end of the day Major League Baseball makes that call, and we're going to respect that."
Instead, the Mets wore their black caps with blue brims and a blue-and-orange interlocking "NY" when they took the field to face the Cubs.
Wright, though, was seen in the dugout early in the game wearing a first responder hat.
The Mets held a 24-minute ceremony of remembrance under dimmed stadium lights before the game. Fans held electronic candles as bagpipers and drummers stood on the infield and first responders lined the basepaths. Each of the Mets and Cubs escorted a member of "Tuesday's Children," a charity for families affected by the attacks, onto the field and they stood with the uniformed emergency-service workers.
A 30-by-90 metre flag was held by first responders and victims' family members.
Marc Anthony sang the national anthem, as he did on Sept. 21, 2001. Mike Piazza, who hit an uplifting homer in the eighth inning to help the Mets beat the Atlanta Braves that night, caught a ceremonial first pitch from New York native John Franco, a teammate on the 2001 squad.
The caps worn during the ceremony will be autographed and sold on Mets.com. Proceeds will be distributed to charities through the Mets' foundation.