However, the FIFA Congress confirmed the existing suspensions for Kuwait and Benin over government interference in their football associations.
Infantino told delegates the decision on Indonesia, one of Asia's biggest football markets, was taken by the FIFA Council after the government agreed to lift a decree considered to constitute unacceptable interference in the football federation.
"The government of Indonesia has advised us that the decree that was causing the suspension had been lifted," said Infantino.
The Asian Football Confederation welcomed Indonesia back into the "Asian football family" but said it would continue to fight any government interference in the running of the game.
"... the AFC Executive Committee reiterated this week their continued stand against government intervention in sport generally and football in particular," the regional governing body said in a statement on Saturday.
"As at their meetings in Delhi last November, Doha in January and Kuala Lumpur in March, the AFC Executive Committee in Mexico City made it clear that there was no place or justification for government interference."
FIFA stepped in to ban the country in June after a long-running row between the government and the local football association (PSSI) over which teams should be entered into the top-flight domestic league.
The government suspended the PSSI after they ignored requests to ban two teams whose owners failed to meet their new governance regulations.
FIFA, after repeated warnings to resolve the row, then banned the country, ruling them out of the joint 2018 World Cup and 2019 Asian Cup qualifying campaign.
Infantino added that the cases involving Kuwait and Benin would be resolved swiftly.
"I'm very sad to be here and have to propose to you that we suspend two associations," said Infantino. "On the other hand, we need to protect our associations from government interference, it is one of our major tasks."
The Kuwait FA (KFA) was suspended by FIFA in October after football's governing body said a draft sports law constituted interference in the nation's football association.
(Writing by Brian Homewood; Additional reporting by Peter Rutherford; Editing by Ken Ferris/Ian Ransom)
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