We don't know Godhead's limits so i don't think there's a straight answer to this fight. It was implied to be the supreme being more than once, and it gave Adam the power to blink the universe in and out of existence, but that's just about it. If we do take the statements as genuine, then the Godhead is the same being as the Presence, given a different name (pretty much like the Unnameable One in Martian Manhunter #4), in which case it should win since the Presence is > GEB.
He's close but not exactly equal. Because GEB was already imprisoned at the beginning of the story (and it had to be the Presence who imprisoned him). Not to mention that after the Presence and GEB "stalemated", we see the Presence operating in DCU but not GEB (which proves that the Presence eventually defeated/contained him).