A name we're not seeing here is Francis. Let's say he either wins at Pavia or manages to sidestep the disaster somehow. The French claims in Italy stay active, the kingdom of France isn't paralyzed by his captivity, and the enormous ransoms aren't paid to Charles. Of course, that's not the end of anything. But let's say it critically weakens Charles for the other tests of his reign, so that he's constantly having to commit resources to Italy to counter Francis and the pope. Each time another foe appears, his resources are just a bit more drained, the battle is just a bit closer, until finally one or the other of them overwhelms him at a crucial point. Let's say there's bad luck in Hungary. Nothing as dramatic as a bad outcome of the Siege of Vienna. Just, bad luck in Hungary.
Maybe it becomes apparent at that point the institutions of the empire and the Habsburg heirs cannot do the job. Or, maybe the Ottoman Sultan simply says they can't be the Holy Roman Empire any more because he is the unique heir of ancient Rome, and that's the price he exacts to go away.
Anyway, that's my thinking.