Coach Thomas Tuchel's team have 15 points from five successive wins, clear of Hoffenheim, who lost 2-1 at home to Bayern Munich, and Hanover 96, 4-1 winners over visiting Werder Bremen.
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"With such a performance we could be playing in the (English) Premier League," said Tuchel, the Bundesliga's youngest coach at 37 and whose tactical acumen has won widespread praise this season.
"The fans were great tonight and they were rewarded with two goals. It is just fantastic," he told reporters.
The 20-year-old Holtby, whose father is English and who has attracted the interest of Premier League clubs, repaid his coach's trust, heading in at the far post to break the deadlock against defence-minded Cologne in the 72nd minute.
Hoffenheim could have grabbed a second just before half-time but Sejad Salihovic's free-kick from 32 metres rattled the post.
Thomas Muller's 62nd-minute leveller and Van Buyten's late winner, when he flicked the ball into the net with his knee, gave Bayern their first league goals and win since August 20.
"We did have a bit of luck today but we sort of forced it," said Bayern coach Louis van Gaal. "We put them under so much pressure that we deserved this victory."
"He could be out for a longer time (than initially thought)," Bayern director Karl-Heinz Rummenigge told reporters.
Last season's runners-up Schalke 04 will be desperate to pick up their first points of the season after four consecutive defeats when they travel to Freibu
