Messi scored his 15th goal of the MLS season.
Inter Miami are five points ahead of second-placed FC Cincinatti in MLS's Eastern Conference.
Mexican side Monterrey sent Lionel Messi and Inter Miami crashing out of the CONCACAF Champions Cup on Wednesday after completing a 5-2 aggregate victory in their quarter-final clash.
Gerardo Martino fielded a heavily second-string line-up with Lionel Messi's former Barcelona team-mates Luis Suarez, Sergio Busquets and Jordi Alba also on the bench.
Inter Miami were beaten 6-0 few nights ago at the hands of Cristiano Ronaldo's Al-Nassr, with Lionel Messi making a cameo off the bench.
FC Cincinnati led the way into the Major League Soccer playoffs on Wednesday as the slim post-season hopes of Lionel Messi's Inter Miami took a hit with a goalless draw against Nashville
In his first game against a Major League Soccer club, Messi was simply too much for Atlanta to cope with.
Lionel Messi announced his arrival at Inter Miami in style as the World Cup-winner scored in stoppage time to hand his team all three points in a Leagues Cup group fixture against Mexican side Cruz Azul on Saturday.
Lionel Messi made a Hollywood start to his career in America, scoring a last-second winner in his debut game for Inter Miami on Friday.
Martino, former coach of Messi with Barcelona and Argentina, said he had spoken to the seven-times Ballon d'Or winner and former Spain midfielder Busquets about their impending move to the Major League Soccer club