Luke didn't defeat the Dark Side. He overcame it, that one time. But he was alreary using the Dark Side before that. To quote the script for Return of the Jedi.
"Luke looks momentarily toward the Emperor, then back to Vader, and realizes he is using the dark side. He steps back, turns off his lightsaber, and relaxes, driving the hate from his being."
But the Dark Side isn't a one and done thing. Luke didn't get a 'Get Out of Dark Side Free' card after that. If anything, because he's used it once, it's always going to be a problem for him. It's like Anakin. He didn't just suddenly start using the Dark Side. He used it once, then twice, the a third, fourth etc.....until finally in ROTS he falls completely.