Despite missing the better half of the first three months of the campaign, Gómez still managed 11 Bundesliga strikes, placing him as third top-scorer in the league for the club. He made an appearance as a late substitute in Bayern's 2–1 Champions League Final victory over German rivals Borussia Dortmund on 25 May at Wembley Stadium in London. He scored a second-half brace in the DFB-Pokal Final on 1 June as Bayern defeated Gómez's former club Stuttgart 3–2 at the Olympiastadion in Berlin. The win secured a 16th DFB-Pokal trophy and an unprecedented league, cup and European cup treble for the Bavarians. He finished the 2012–13 season with 11 goals in 21 league appearances,