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.
Inter Miami's charge towards Major League Soccer's single-season points record suffered a setback on Saturday after a last-gasp injury-time equalizer from James Sands snatched a 1-1 draw for New York City FC against the Eastern Conference leaders.
The Argentinian superstar Messi came close to a game-clinching goal in the 83rd, but his angled effort was blocked by Atlanta goalkeeper Brad Guzan and Suarez's attempt to tap in the rebound was also denied.
The eight-times Ballon d'Or winner hadn't played since injuring his right ankle during the Copa America final on July 14, when he helped Argentina to victory over Colombia.
The league's top talents will face the Mexican League All-Stars on July 24 at Columbus, Ohio.
Messi's star turn raised the profile for MLS in the United States.
Inter, upset at home by Atlanta on Wednesday, appeared to be heading for another costly loss after a 68th-minute Luis Suarez own goal left St.Louis 3-2 up heading into the final minutes.
Lobjanidze stunned a star-studded Miami line-up with two long-range strikes either side of half-time to fire Atlanta into a 2-0 lead.
Inter Miami rested Lionel Messi and Luis Suarez but still managed to extend their unbeaten run in Major League Soccer to 10 games with a hard fought 2-1 win at the Vancouver Whitecaps on Saturday.
Messi, 36, has become the face of MLS since joining Miami last July, but he has yet to make an appearance in Vancouver.
Despite the return of Lionel Messi to the starting line-up, after he missed the 0-0 draw at Orlando on Wednesday, Miami struggled to create chances against a very well organized D.C. defense.
Lionel Messi's record $20.45 million annual salary from Inter Miami makes him by far the best paid player in Major League Soccer but also puts him ahead of the entire squads of 25 of the league's clubs, according to data released by the MLS Players Association on Thursday.
Inter Miami's five-match winning run came to an end on Wednesday as, without the injured Lionel Messi, they were held to a 0-0 draw at Orlando City.
Messi briefly left the field for attention after a heavy challenge and while the Argentine was on the sidelines, his team won a free-kick in the area -- where the World Cup winner can be so deadly.
