Inter Miami play-off hopes hit while Cincinnati secure top seed in MLS
Messi, who had missed Wednesday's US Open Cup final defeat to Houston and last week's draw in the league at Orlando, was again missing with the injury which has troubled him since mid-September.
Without the Argentine and his former Barcelona teammate Jordi Alba, who is out with a hamstring injury, Miami looked short of ideas.
After a lacklustre game, New York struck in the 77th minute with a fine individual goal from Santiago Rodriguez.
The Uruguayan brought down a long ball from Tayvon Gray and held off two Miami defenders as he turned before blasting into Drake Callender's near post.
Miami had not managed an effort on target in the entire 90 minutes but then in the fifth minute of stoppage time defender Tomas Aviles rose to head in a Robert Taylor corner.
The home side were desperately close to grabbing a dramatic late winner when David Ruiz burst into the box, but his drive from close range bounced out of the underside of the bar.
Miami are in 13th place in the East, four points behind ninth-placed Montreal, who occupy the final playoff spot, but with a game in hand on the Canadian team.
Miami head coach Gerardo Martino said that Messi has been training but separate from the team and that he was improving his fitness but remained a doubt for Wednesday's trip to Chicago.
"He is training on the field, different from the group but he is feeling better and better," said Martino.
"On Tuesday we will evaluate him because we make the trip to Chicago. But we are not going to take any kind of risk. If we interpret from the talk with the player and the doctors that the risk is still present, the player will be out of the game," he said.
"But I can't say today that he is out of the Chicago game because he is training better and better and there is nothing left to do but evaluate him day by day," he added.
NYCFC are a point ahead of Montreal in eighth place. Wayne Rooney's DC United are level on points with Montreal after drawing 2-2 at Vancouver thanks to Polish midfielder Mateusz Klich's 62nd-minute equaliser.
That result meant that Nashville, who drew 0-0 with Seattle, claimed the seventh first-round playoff spot in the East.
A big night for Cincinnati saw them win the Supporters' Shield for the best regular season record, after their 3-2 win over Toronto secured them the top seed in the playoffs.
The Supporters' Shield is the first trophy for Cincinnati since they joined MLS in 2019, a year after they won the second-tier USL title.
Cincinnati took a 2-0 lead at the East's bottom club Toronto, with two close-range goals from USA international striker Brandon Vazquez.
If Cincinnati's thoughts were turning towards silverware they were given a shock as Toronto fought back before the break with a pair of goals from Jonathan Osorio.
But a left-foot finish in the 72nd minute from Aaron Boupendza, after good work from playmaker Luciano Acosta, made sure of the win and Cincinnati's first honors in MLS.
Cincinnati had finished bottom overall in MLS in each of their first three seasons in the league but will now have home-field advantage throughout the play-offs and for the MLS Cup final should they qualify.
Brazilian forward Joao Klauss scored twice as St Louis City, top of the Western Conference and assured of a place in the playoffs, beat Sporting Kansas City 4-1.
The Portland Timbers, seventh in the West, fought back for a 3-3 draw at Los Angeles Galaxy after Chilean Felipe Mora struck a 76th-minute equalizer to extend their unbeaten run to seven games.
Forward Julian Hall became the second youngest debutant in MLS history when he made his New York Red Bulls' debut in the 1-0 defeat to Chicago Fire FC, appearing as an 81st-minute substitute at Red Bull Arena.
At 15 years, 190 days, Hall became the youngest player to appear in an MLS match since Freddy Adu played for DC United in 2004 at 14 years, 306 days old.