Doomsday did not have flight ability until after he fell to earth and went through further metamorphosis, so until then he had no means of propelling himself back to Earth (he could have the flight power inducing metamorphosis while floating in the space but that is not what we see in the movie).
Ideally, the shockwave from the nuclear explosion should have pushed them both further up into the space. But if we assume there was no air so high up there to create the shockwave, then either both of them should've fallen back to earth or both should've kept floating in space. There doesn't seem to be a reason for one of them to fall back while the other did not.
So why did Doomsday fall back to earth after the nuclear blast but Superman didn't?