Ha, the show's first blind contestant, beat fellow finalist Josh Marks to take home the grand prize of $250,000 and a cookbook deal.
Earlier, she had impressed judges Gordon Ramsay, Joe Bastianich and Graham Elliot with her Thai papaya salad with crab, braised pork belly with rice, kale and maitake mushrooms, and a dessert of coconut lime sorbet.
Ramsay described the choice as "the most difficult, the most compelling decision" the judges had ever had to make.
"I just can't believe it, I'm the MasterChef," Ha said afterwards.
"This has been the most amazing experience, seriously. After all the obstacles I've been through, going up against such awesome, amazing cooks... I'm living proof that dreams come true against all odds."
Meanwhile, Marks described her as a "tough competitor", adding that he loves and respects her.
"I will never give up on my dream - it will come true," he said. "Whether I'm the MasterChef or not, it's definitely coming true."
MasterChef was renewed for a fourth season by Fox in July.