The late strike gave the Herons a franchise-record three-game winning streak and extended Miami's unbeaten run to six games (5-0-1). With the victory, Inter Miami (9-9-5, 32 points) moves into fifth place in the Eastern Conference.
Toronto FC (3-15-6, 15 points) lost their sixth consecutive game, and Tuesday's result could be the most disappointing defeat yet for the last-place team. Despite playing over half the game with a 10-man lineup following Kemar Lawrence's 37th-minute red card, Toronto created the majority of the attacking pressure both before and after Lawrence's ejection.
Toronto thought it had scored the go-ahead goal in the 87th minute when Inter Miami goalkeeper Nick Marsman rushed a clearance kick that was intercepted by TFC forward Jacob Shaffelburg. Marsman seemingly stopped Shaffelburg's hard shot directly on the goal line, and reviews were inconclusive as to whether the ball was fully in the net.
With the game still scoreless in extra time, Makoun capitalized when he was pulled down in the box by Toronto defender Chris Mavinga. Makoun was chosen to take the penalty himself, and the 21-year-old converted for his first career MLS goal.
Inter Miami were themselves almost reduced to 10 men in the 14th minute, as midfielder Gregore was seemingly ejected for pulling down Toronto's Richie Laryea in the box. However, Laryea was ruled offside after a video review, thus erasing both Gregore's red card and the penalty kick that had been awarded to Toronto FC.
Marsman made four saves for his fourth consecutive shutout. Inter Miami has gone 388 minutes without allowing a goal, and Kieran Gibbs' own goal has been the only concession of any kind surrendered in the Herons' last 492 minutes of play.
Toronto midfielder Tsubasa Endoh was substituted out of the game in the fifth minute due to an apparent leg injury.