Messi was left seething in the aftermath as he felt his team should have been awarded a penalty in the end. He approached the referee and according to 'Ole' via Mundo Deportivo, told him: 'You're a mean-spirited son of a beep....!
The former Barcelona and PSG forward escaped a sending-off and was booked instead, even though the match had ended.
Before the incident, Charlotte had a goal ruled out for offside after Kerwin Vargas put the ball in the back of the net from close range.
The forward went on to miss a glorious opportunity in the 96th minute, curling an effort wide of the post.
Messi's rant comes just a week after he struck
Miami was also held to a 1-1 draw by New York City on that occasion, with James Sands scoring a 95th-minute equalizer for the hosts.
Speaking to the media post-game, NYCFC head coach Nick Cushing addressed the crowd of 44,738 that came to see Messi play.
'I hope they enjoyed the game,' Cushing said. 'I hope they see the level of the league is exciting. Two teams both attacking each other. I was proud that we created chances in the game.
'One thing I will say is, our support section and every New York City fan that came tonight pushed us to the end. They supported us through the game, they gave us life and energy.'
Despite three straight draws, Miami is close to winning the Supporters' Shield, a title given to the team with the best regular-season record.
They remain top of the Eastern Conference and are eight points clear of second-placed Columbus Crew with three games left.
The top two will lock horns when Miami visits the Lowe.com Field on Wednesday evening local time.
