But Reds coach Airton Andrioli won't let his striker's rush of blood get him down after captain Craig Goodwin and Jovanovic came off the bench to inspire an extraordinary win at AAMI Park on Sunday evening.
Jovanovic will miss the first leg of Adelaide's semi-final in two weeks after celebrating scoring his winner by ripping off his shirt - picking up a second yellow card in 60 seconds after being booked for his role in an all-in melee.
"Obviously he is now a little bit disappointed, we are also disappointed," Andrioli said.
"But I will take that any day of the week - coming on and scoring two goals."
Jovanovic's goal was his 11th of the season and earned him the shared golden boot award with Auckland's Sam Cosgrove.
Adelaide finished behind premiers Newcastle and ahead of Auckland FC, Melbourne Victory, Sydney FC and City.
The Reds also earned a play-off spot for next year's expanded Asian Champions League Elite competition.
"I spent a lot of time waiting for an opportunity to be at this level and I always felt if I got an opportunity, if I have what it takes to maybe do something special," first-year coach Andrioli said.
"I want to thank all the people that didn't believe in us because I think that was a great advantage for us."
While Adelaide enjoy a week off, City cost themselves a home elimination final and travel to face Auckland, with Victory to host Sydney.
"It wasn't just the last 180 seconds, obviously there was big moments with the goal, but we weren't good enough tonight as a whole," Melbourne City coach Aurelio Vidmar said.
"Opportunity lost for sure."
City defender Samuel Souprayen (left knee) was forced off in the 41st minute.
With Socceroos coach Tony Popovic in the stands, City's Marcus Younis opened the scoring in the 17th minute.
Younis rifled an unstoppably fierce strike inside the near post, his eighth goal since signing on loan from Denmark's Brondby in January.
The 20-year-old Australian performed a "call me'' celebration, seemingly referencing his desire for a maiden national call-up.
Goodwin returned from a groin injury in the 78th minute for his first game in 77 days, and a minute later provided the assist - via a scuffed shot - for Jovanovic to pounce and fire home.
The all-in scuffle started after Jay Barnett fouled and shoved Younis into the ground, with Adelaide's Jovanovic and Anselmo booked along with City's Aziz Behich and German Ferreyra.
Vidmar noted Barnett should have received a second yellow card.
Goodwin burst forward on the break after the melee and found Ryan White, who teed up Jovanovic to bury the winner.
