The 30-year-old was granted permission to return to Catalonia on Saturday after playing the full 90 minutes of his side's 1-0 win against Russia in Moscow.
Messi, who has already played 22 games for club and country since the start of the season, will now skip next week's friendly with Nigeria to instead rest up.
Asked about his decision, the Barca superstar told reporters: "We talked to [Jorge Sampaoli]. We play many games in the season – the Champions League, the Copa del Rey, La Liga, plus everything about the national team and the trips. I want to get to the World Cup in the best way."
Messi has scored 19 goals so far this term, including a hat-trick against Ecuador last month to send Argentina through to Russia 2018.