A David Wheater header from Jay Spearing's cross in the 15th minute proved to be the difference between the sides, although the Trotters did have chances to double their advantage.
"I'm very happy with that result. I said to the team before the game that particularly with derbies, the first 25 minutes are always crucial and it's imperative that you start well," Freedman told the club's official website.
"Throughout the opening stages, I felt we were the better team. We were confident and calm on the ball and we managed to get that all important goal."
Bolton currently occupy 17th spot in the Championship.