On 26 December it was announced that A-League expansion club Melbourne Heart had signed the then 17-year-old for their inaugural A-League 2010–11 season. He made his debut for the club in a friendly against Geelong All Stars XI and also scored his first goal in that match. He also took part in the friendly against Everton FC in which Heart lost 2–0. He made his debut for Melbourne Heart in the opening round of the 2010–11 A-League season against Central Coast Mariners at AAMI Park. During May 2012 it was announced that Serbian side Red Star Belgrade was scouting him.
Eli Babalj made his return appearance to the A-League for the Melbourne Heart away to the Western Sydney Wanderers on Australia Day, 26 January 2013 as a 2nd half substitution.
AZ
On 19 April 2013, Dutch club AZ Alkmaar completed the signing of Eli for a fee believed to be in the region of $200,000.
On 24 July 2015, Alkmaar confirmed that they would allow Babalj to go out on loan back to Australia to Adelaide United for the 2015–16 A-League season. This would be Guillermo Amor's first signing for Adelaide as the new manager. Babalj made his debut for Adelaide United as a substitute in the 2015 FFA Cup in Darwin against Darwin Olympic. He also scored his first goal to help Adelaide to a 6–1 win. On 22 January 2016, Babalj ruptured his anterior cruciate ligament against Brisbane Roar, ruling him out for the remainder of the A-League season.
Adelaide United
On 7 February 2017, after training with Adelaide United since late January, Babalj joined Adelaide United once more until the end of the season.
Babalj signed with Indian Super League club ATK for the 2018–19 season. He made his first appearance on 28 November 2018 against FC Goa, coming on as a substitute in the 68th minute. The match ended 0–0.
International career
He has represented Australia at U-20 level during the 2010 AFC U-19 Championship qualification for the 2010 AFC U-19 Championship. He played in 4 qualification games, scoring 3 goals, against Singapore, and two against Chinese Taipei. Babalj also represented Australia at the AFF U-19 Youth Championship. He scored against Vietnam and the winning goal in the final of the AFF U-19 Youth Championship against Thailand. He made his debut for Australia's senior team on 14 November 2012 in a friendly against South Korea. Babalj was selected in the Socceroo's squad for the East Asian Cup qualification round. He started his first game for Australia against Guam in a 9–0 win, scoring a double before being substituted.
