The commercial can be viewed here.
Sounds an awful lot like him. And one of the Youtube comments agrees with me…which actually makes me more inclined to think it’s not him, Youtube comments being what they are. 
Yeah, he’s been the Cottonelle puppy for years now.
According to IMDb, among Zach Braff’s credits is “TV commercial for Cottonelle (voice over as the puppy; 2003-2006)”