The buyer or seller's name was not disclosed, but there is speculation it was owned by actor Nicolas Cage.
It is the first time a comic book has broken the $2m barrier. The issue was published in 1938 and cost 10 cents.
About 100 copies of Action Comics No 1 are thought to be in existence, and only a handful of those are in good condition.
Another copy of the same issue sold for a then record-breaking $1.5m in March last year.
But that one was not in as good condition as the copy that sold on Wednesday through New York-based ComicConnect.
It is said to have been stolen in 2000 and was thought lost until recovered in a California storage shed in April this year - just like an issue owned by Nicolas Cage.
The Hollywood star - who has a son called Kal-El, the Man of Steel's birth name - bought his copy of Action Comics No 1 for $150,000 in 1997.
Connoisseurs of the comic world say this type of investment has become popular during troubled economic times because rare collectibles hold their value more reliably than property or shares.