for the first movie, Pacino was pretty unknown and was up with two other Godfather actors for best supporting actor: Caan and Duvall--both of which also gave great performances. So I think the three split the Godfather vote.
and as far as the second, I agree that he and Jack for Chinatown probably knocked each other out of contention. Plus, Art Carney's performance was great, AND he was the sentimental favorite because of his Honeymooner's background.
I agree that both Pacino performances were great, but they were both very subtle. They weren't as showy as some of the other peformances. Also, because he was still pretty new, people didn't know if Pacino wasn't just playing himself.