Messi tucked the 84th minute spot kick into the corner to complete the comeback for Miami and earn them a place in the last four.
Too often Messi, who played the full game, was trying to create by himself while crowded out by Toronto defenders but did he test Johnson with a low shot in the 77th minute after working some space for himself.
A 57th-minute strike from Los Angeles-born El Salvador international Nathan Ordaz handed LAFC a precious advantage heading into next Wednesday's return leg in Florida.
Messi had missed Argentina's World Cup qualifiers in South America during the recent international window after picking up an adductor strain in Miami's most recent Major League Soccer game, a 2-1 win at Atlanta on March 16.
Veteran Haiti international Fafa Picault headed in the winning goal in the 89th minute to give Miami a precious victory that extended their unbeaten start to the season.
It marked the third straight game that Messi failed to feature for Miami after he did not travel to Houston for last week's 4-1 win in MLS before watching the 2-0 victory over Jamaica's Cavalier in the CONCACAF Champions Cup first-leg game on Thursday.
Luis Suarez scored a goal and assisted on three others to lead Inter Miami to a dominant 4-1 victory over the host Houston Dynamo on Sunday night.
Messi scored in the 1-0 first-leg win in icy Kansas City last week and it took him only 19 minutes to find the target at a much warmer Chase Stadium in Fort Lauderdale in the return.
The Argentine World Cup winner was caught on camera in a confrontation with NYCFC assistant coach Mehdi Ballouchy after the final whistle.
Messi struck in the 56th minute at Children's Mercy Park, showing superb individual skill before rifling a low angled shot past Sporting goalkeeper John Pulskamp.
The United States National Weather Service has issued a winter storm warning for the region, which includes parts of east-central and northeastern Kansas and central and west-central Missouri.
For now, the Argentine is focused on Inter Miami’s upcoming season and the FIFA Club World Cup in 2026.
Rumours linking Neymar with a move to Miami to recreate the old 'MSN' Barcelona front line with Messi and Luis Suarez have resurfaced in recent days.
Mascherano, 40, is a former teammate of Miami star Lionel Messi. The two were teammates at FC Barcelona from 2010-18.
Miami had won the regular season campaign with a record points total but after losing twice in the best-of-three series, the MLS Cup favourites and their eight-times Ballon d'Or winner are out.
Portuguese winger Xande Silva blasted home a sensational winner for Atlanta in the fourth minute of stoppage time in front of 68,455 home fans at the Mercedes-Benz Stadium to level the best-of-three postseason series 1-1 and set up a winner-take-all game three in Miami next Saturday.
Miami started with all their big-name stars, including Lionel Messi, on the bench but the Argentine was introduced in the 61st minute to the delight of many in the Toronto crowd.
Messi had been subdued until the 45th minute when he put Inter ahead -- chesting down a long ball into the box and getting a lucky bounce off Crew defender Malte Amundsen before poking home.
Messi tied Saturday's match in the 67th minute when he lasered a shot from beyond the box that evaded diving Charlotte goalkeeper Kristijan Kahlina to make it 1-1.
