Yoda was already beaten by that point. Despite seemingly able to hold up to Darth Sidious at first he was put on the defense during the whole fight. And that despite him giving himself over to the force fully and using it as much as he could.
He still tried to press on, but was weakening visibly more and more during the fight. _In the novel it is explained that he saw that he was fighting the wrong war the whole time......that he tried (and the jedi order itself tried) to reenact the last war while the sith had....adapted and became something else, something more. Something he (and they) could not beat.
When Yoda fell he on purpose did not try to come up again and instead fled as he already saw (even in the film) that he was not able to overcome the dark lord of the sith. Soemthing / someone else was needed for that. Someone trained differently than himself and Obi Wan.