McBreen's first goal of 2012–13 came seven minutes after entering the Mariners's 1–0 win at home to Perth Glory as a 63rd-minute substitute, in what was his first appearance of the season. He recorded the first hat-trick in the Mariners' history in their 7–2 home win over Sydney FC on 3 November 2012, scoring in the first half with a penalty kick and in the second half with a close range finish and a header from Josh Rose's cross. This marked the start of a run of 14 goals from 15 matches, helping the Mariners to second place in the 2012–13 A-League table and thus a place in the finals series. With 17 goals McBreen won the A-League Golden Boot, awarded to the division's top scorer. In the semi-final of the finals series he scored the only goal in the Mariner's 1–0 win over Melbourne Victory on 14 April 2013 with a powerful shot in the 42nd minute. One week later he scored the second goal with a 68th-minute penalty kick as the Mariners beat Western Sydney Wanderers 2–0 at Sydney Football Stadium in the 2013 A-League Grand Final. This was the first time the Mariners had won the A-League Championship, and McBreen was awarded the Joe Marston Medal, given to the man of the match of the Grand Final, before being named as a substitute in the PFA A-League Team of the Season. He made six appearances in the team's run to the round of 16 of the AFC Champions League, when they were beaten 5–1 on aggregate by Guangzhou Evergrande of the Chinese Super League. McBreen signed a new contract with the Mariners for the 2013–14 A-League in May, having scored 19 goals from 33 appearances in 2012–13.