Despite the arrival of centre-back Dante from Borussia Mönchengladbach in the summer of 2012, Van Buyten became an integral member of the back-line for the Bavarians during the 2012–13 campaign, part of a three-man rotation in the centre of defense with Dante and Jérôme Boateng. On 6 April 2013, with a 1–0 defeat of Eintracht Frankfurt thanks to a goal from Bastian Schweinsteiger, Van Buyten celebrated his third Bundesliga championship with Bayern, clinching the club's 23rd national title. Van Buyten played the full 90 minutes in the club's 3–0 second leg semi-final victory over Spanish champions Barcelona on 1 May, clinching a resounding 7–0 aggregate victory and a place in the Champions League final against fellow Bundesliga side Borussia Dortmund. Van Buyten is the first Belgian player in a Champions League final.