Messi had been out of action since sustaining an ankle injury in Argentina's 1-0 win over Colombia in July's Copa America final.
As a result, the 37-year-old had not played for Inter Miami since scoring in a 3-3 draw against St Louis City on June 2.
Speaking ahead of Saturday's clash with Philadelphia, Inter Miami boss Tata Martino confirmed Messi would be available for selection despite missing Wednesday's training session through illness.
Although he had been out of action for around two months, Messi was deemed fit enough to start the fixture at Chase Stadium in Fort Lauderdale.
Messi makes MLS history
Messi required just 26 minutes to get on the scoresheet, shifting the ball onto his right foot before guiding a low shot into the bottom corner.
Just four minutes later, Messi added to his and Inter Miami's tally, sweeping the ball past Andrew Rick after being teed up by Jordi Alba.
Not only did Messi give his side a two-goal advantage, but he also created a piece of MLS history with his quickfire double.
As a result of the brace, the former Barcelona star became the fastest player to reach 15 goals and 15 assists in MLS history.
Messi achieved the feat in just 19 MLS matches, smashing the previous record which was held by Sebastian Giovinco, who registered 15 goals and 15 assists in his first 29 MLS appearances.
After setting a new record, Messi went on to grab his 16th MLS assist in the second half, laying the ball off for Luis Suarez to add his name to the scoresheet.
When will Messi play next?
The victory moved Inter Miami onto 62 points, leaving them 10 points clear at the top of the Eastern Conference standings.
Messi and Inter Miami will be back in action in midweek, with Martino's side set to travel to the Mercedes-Benz Stadium for a meeting with Atlanta United.
After playing 90 minutes against Philadelphia, it remains to be seen whether Messi will start just days after making his return to action.
Inter Miami and Messi will also take into account the fact that the Mercedes-Benz Stadium has artificial turf, and such a pitch has previously been linked with an increased risk of injury.