Germán Berterame also found the net for Inter Miami, who continued to build momentum as the MLS Cup Playoffs approached. Fafa Picault scored a late penalty for Atlanta, but it was not enough to prevent the hosts from suffering another disappointing result.
Berterame breaks the deadlock before half-time
The contest began cautiously, with both teams looking for openings while maintaining their defensive shape.
Messi threatened in the 41st minute with a free-kick that Atlanta goalkeeper Lucas Hoyos saved. The Argentine's involvement proved decisive shortly afterwards, however, as Inter Miami found the breakthrough just before the interval.
Messi headed the ball towards Luis Suárez, who worked space inside the penalty area before delivering a cross from the right. Berterame connected with a header at the back post in the 45th minute to give the visitors a 1-0 lead.
The goal rewarded Miami's growing attacking threat and ensured Atlanta went into half-time trailing despite having competed well during the opening period.
Messi strikes twice in four minutes
Inter Miami increased their advantage in the 56th minute through their captain.
Messi carried the ball forward from the right, combined with Berterame and continued his run into the penalty area. After working past a defender, he finished with a low left-footed effort to make it 2-0.
The eight-time Ballon d'Or winner struck again in the 60th minute, producing another moment of individual quality. Suárez delivered a superb outside-of-the-foot pass into space, allowing Messi to race towards goal, evade a defender and finish past Hoyos.
The brace took Messi to 25 goals in the MLS regular season, strengthening his position at the top of the league's scoring chart.
Berterame played a crucial role in the second-half goals, assisting Messi's first strike and contributing to the attacking movement that created the second.
Messi reaches another MLS milestone
Messi's influence extended beyond his goals. His involvement in the opening goal helped him register his 15th assist of the regular season.
That achievement made him the first player in MLS history to record at least 15 assists in three consecutive seasons.
The Argentine has continued to combine goalscoring with creative playmaking, providing Inter Miami with a decisive attacking presence as the team pursues further success.
The result also marked Miami's third consecutive league victory, strengthening their momentum ahead of the playoffs.
Picault scores late consolation for Atlanta
Atlanta United continued searching for a response, but Miami's three-goal advantage left the home side with a difficult task.
Fafa Picault converted a penalty in the 89th minute to reduce the deficit to 3-1. Atlanta attempted to build on the goal during the closing stages, but Inter Miami held on to secure all three points.
Despite the defeat, Atlanta created opportunities of their own and tested Miami's defence. Their inability to convert those openings, however, proved costly against a side that made the most of its decisive attacking moments.
What the result means
The victory moved Inter Miami to 55 points from 30 regular-season matches, with a record of 15 wins, five defeats and 10 draws. It also continued their three-match winning streak as the defending champions prepared for the closing stages of the campaign.
For Atlanta United, the defeat added to their struggles in the Eastern Conference, leaving their hopes of reaching the playoffs under increasing pressure.
Messi's brace was the headline moment, but Miami's collective attacking play, Berterame's contribution and Suárez's creativity were equally important in securing the result.
Full-time: Atlanta United 1-3 Inter Miami
Goalscorers:
• Atlanta United: Fafa Picault 89' (pen)
• Inter Miami: Germán Berterame 45', Lionel Messi 56', 60'