Jovanović made his official debut for Partizan in 20 fixture match of the 2016–17 Serbian SuperLiga season against Čukarički, played on 11 December 2016, replacing Uroš Đurđević in 89 minute.

[5] In 2017, Jovanović was optionally loaned to satellite club Teleoptik on dual registration until the end of 2016–17 season in the Serbian League Belgrade.

On 17 August, Swiss Super League team FC Basel announced that they had signed Jovanović on a four-year contract.

Jovanović played his debut for his new club in the Swiss Cup first round game on 20 August, coming on as a substitute in the 58th minute.

He scored his first goal for his new team in the same game, a penalty in the 63rd minute, as Basel went on to win 8–1 against amateur club FC Saint-Blaise.