Braff, who recently announced that he is to leave the ABC show at the end of the upcoming season, split from Roswell actress Shiri Appleby last November.
However, the couple were seen cuddling at a California restaurant last month and friends have now confirmed that they are back together.
A source told Star: "Zach and Shiri have insane chemistry. When they broke up it was because Shiri wanted something more serious and Zach wasn't ready.
"Shiri still has her doubts, but neither of them can call it quits."
Braff was previously linked to actresses Mandy Moore, Bonnie Somerville and Drew Barrymore.