Ford blew up the MUTO nest and this gave Godzilla the window needed to get his bearings and counter attack. This coupled with the female MUTO taking off after the HALO drop team's extraction of the bomb both to reclaim it and likely avenge her offspring, gave Godzilla his opening to kill the male MUTO and lighten his odds. An injured and worn out Ford and Godzilla come across one another and share a gaze, both clearly studying and taking note of each other. Godzilla is overtaken by the dust and Ford, now having his second wind, manages to haul himself out to the harbor with a busted leg to get the nuke bearing boat out to sea. Afterwards we all know what happens.
Was it an Androcles' Lion scenario, like the Aesop of the man who pulled a thorn from a lion's paw and was later protected by it, with Godzilla intentionally saving Ford?
Was it just a happy coincidence that Ford happened to distract the female MUTO in just the right manner for Godzilla to sneak up and ambush her?
Considering Godzilla incidentally saved Ford earlier with the first atomic breath firing, was that case accidental and this was intentional?
When Godzilla noticed Ford, did he know this was the human which had angered the MUTOs and destroyed the nest; or was he just passively noticing a human nearby?
The movie never gives a concrete answer because exactly how aware Godzilla is to humanity is very ambiguous in this movie. While the later MV films would add some clarity, I always liked how this film played it in respect to this plot. And no matter which way it's sliced, it doesn't really cause anything in the movie to change. That's some smart film-making I don't often see get the praise it does.
*Edit: Rando Yaguchi reminded me of a few other times Godzilla noticed someone, thank you
