Lionel Messi scores but Inter Miami held as rivals secure playoff spots
Elsewhere, the Seattle Sounders, Houston Dynamo, New York Red Bulls, New York City, LAFC and Orlando City all secured their places in the playoffs.
Despite the setback of a third straight draw, Miami -- already assured of a place in the playoffs -- remain top of the Eastern Conference and the Supporters Shield regular season standings.
Charlotte, coached by former Aston Villa boss Dean Smith, took the lead in the 57th minute when a low shot from Brandt Bronico deflected off Karol Swiderski and beat Miami keeper Drake Callender.
The goal added some needed urgency to Miami's approach and Jordi Alba found his former Barcelona team-mate Messi with a cross from the left, but the Argentine's header was straight at goalkeeper Kristijan Kahlina.
The Croatian keeper then did well to keep out a Messi drive from the edge of the box.
Moments later Messi, just outside the area, carved out just enough space for a shot and buried his left-foot drive into the bottom corner for his 15th goal in as many games this season.
Miami thought they had won a penalty in the 77th minute when Diego Gomez went down under a challenge from Charlotte's French defender Adilson Malanda and referee Ramy Touchan pointed to the spot.
Malanda received a second yellow card but he and his team were saved by the VAR, who ruled he had played the ball.
Deep in stoppage time, Miami had a great chance to take all three points when Alba headed across goal, but Luis Suarez under pressure from Kahlina fired over the bar from a yard out.
Miami are on 65 points with three games remaining, champions Columbus Crew have 57 and Cincinnati 56 in the East.
Miami can clinch the Supporters' Shield with a victory or a draw away to Columbus on Wednesday and head coach Gerardo Martino said that frustration with another draw should be kept in perspective.
"We were a team that habitually lost for years, and now, we are a team that habitually wins, and that raises expectations," he said.
"We have worked very hard to change the perception of this team, and we’ve done it having to use many different line-ups due to injuries and national team duty.
"Yes, we are frustrated with three draws in a row... but it's not like we did not have chances to win," he added.
In the 'Hudson River derby', New York City romped to a 5-1 win at the New York Red Bulls with two goals from Alonso Martinez as the visitors led 4-1 at half-time.
The win secured NYCFC a place in the playoffs and other results meant the Red Bulls had the consolation of also getting into the post-season.
Orlando City are also in the mix for a run at MLS Cup after an impressive 3-1 win at FC Dallas and LAFC, beaten by Columbus in last year's final, booked their place in the playoffs with a 2-1 win at FC Cincinnati.
Results in other games meant that Seattle and Houston were sure of their place in the post-season even before their game later on Saturday.