The $412 payment, which includes a $130 line item relating to character rights, hit the milestone within three days on ComicConnect.com, and still has two weeks remaining.
"That $130 cheque essentially created a billion-dollar industry," said ComicConnect co-owner Vincent Zurzolo.
"Without this cheque being written out by DC Comics, there would be no Superman, and thereby no Batman, Wonder Woman, Spider-Man, X-Men, or any of the other characters that came into existence after the concept of the superhero was born with Superman."
The heirs of Siegel and Shuster have been involved in a long-running legal dispute with DC and Warner Bros over the rights to Superman. The Siegels successfully recaptured a portion of the licence in 2008, and the Shusters have the opportunity to do the same next year.
The auction for the Superman rights cheque ends on April 16.