The current owner of the home that once belonged to Puzo's heirs stumbled across the movie gold while tidying up and he has handed over the lost reels to bosses at Boston, Massachusetts-based RR Auction.
The footage covers the first 40 minutes of the classic 1972 Francis Ford Coppola movie, which Puzo adapted from his own book.
Puzo and the director, who shared a Best Adapted Screenplay Oscar, famously fell out over creative differences and when Coppola was ultimately granted final rewrite duties on the movie, Puzo was barred from viewing any of the final cuts or edits.
Instead he was given the film reels after the movie had wrapped as a keepsake.
"It's a remarkable offering of celluloid history," said Robert Livingston, executive vice-president at RR Auction.
Both reels are housed in the original vintage industrial grade Paramount Pictures hinged film reel case.
The upcoming auction also features Marlon Brando’s cue cards from The Godfather and Puzo’s copy of Time magazine from August, 1978, which features an artistic depiction of the novelist smoking a cigar on the cover.
The online auction will begin on 16 June (16) and run until 23 June (16).