Makaay controlled a deflected through ball on his thigh and tucked home past Kasey Keller in the 13th minute while Ballack's perfect strike made it 2-0 to the champions 10 minutes into the second half.
Belgian striker Wesley Sonck pulled one back within 60 seconds but Makaay restored Bayern's two-goal lead with a fine volley in the 69th minute.
A 15th win from 18 Bundesliga games stretched Bayern's lead to nine points, although Hamburg SV can cut that to six if they win at Nuremberg on Saturday.
Bayern have 47 points from 18 matches, with Hamburg on 38 from 17. Werder Bremen, who visit Arminia Bielefeld on Sunday, are two points further back in third.
Bayern's superiority in the first league match after the six-week winter break will be a depressingly familiar
The only surprise was that they did not add to the early lead given to them by Makaay in the first half of a game played in freezing conditions.
Lucio and Ze Roberto each forced desperate clearances after breaking forward, with Gladbach struggling to hold on.
Ballack's well placed free kick from the edge of the box looked to have signalled the end of the contest only for Sonck to drag a deflected Eugen Polanski cross back past Oliver Kahn on the next attack.
Bayern had a tough 120-minute Cup workout against Mainz in midweek but they showed no ill effects as they surged forward in search of another goal.
That came as Makaay waited for Hasan Salihamidzic's long ball to drop and clattered it first time past Keller.
"I was very satisfied with that performance," said Bayern coach Felix Magath. "You could see it was an advantage for us to have that Cup match to find our rhythm."
