A CGC-rated 9.6, or near-mint, example of the Marvel comic Amazing Fantasy No 15 in which he made his debut in 1962 was bid to $3m (£2.17m).
The 11pp story was the work of Stan Lee and Steve Ditko, with cover artwork by Jack Kirby.
Heritage was thrilled with that result on September 8-12, but in its November 18-19 sale it has a copy of Action Comics No 1 of 1938 that featured the debut of Superman which could reclaim the comic book hero top spot.
So popular did the character of Spider-Man quickly become that in March of the following year Marvel issued the first Amazing Spider Man comic – a 9.4 CGC-rated copy of which sold for $201,000 (£145,650) in the September 8-12 Dallas sale.
Other high-fliers in this exceptional auction included, at $480,000 (£347,825), a copy of the very first Batman comic of 1940 with a CGC rating of 6.5, and the original artwork produced in 1969 by Jack Kirby and Joe Sinnott for the cover of issue No 86 of Fantastic Four, which made $400,000 (£289,855).