I decided to bump this because you guys were seemingly forgetting something
Gogeta needed to use the evil inside Janemba to win against him. He even says:
"Every force you create has a echo. Your own bad energy will be your undoing"
And right after that, we see Gogeta using some hocus pocus to stop Janemba from powering up.
I think that Gogeta couldn't beat Janemba for himself, or at least he didn't felt like it.
Even after being punched by a Janemba that was losing power very uickly due to the fact that he was being erased from existence, Gogeta was still budged