The match grew spiteful in the final few minutes of extra time with Youssouf Kone, who had scored Mali's goal, sent off when he received a second yellow card for apparent dissent.
He then appeared to push Argentine referee Mauro Vigliano and needed to be ushered away by his team mates before he trudged off North Harbour Stadium in Auckland.
Andrija Zivkovic opened the scoring in the fourth minute for Serbia, though they could have had at least another three goals as Mali's defence disintegrated.
Mali, however tested Serbia throughout on the counter attack and they got back into the game when they spread the ball to Kone who slammed it from 35 metres out past the diving Predrag Rajkovic to level the game.
The goal rejuvenated Mali and Rajkovic was forced to tip a Soulemayne Diarra rocket from 25 metres over the bar less than two minutes later.
The Serbian captain again saved his side in the 67th minute when Dieudonne Gbakle was through one on one, while the crossbar thwarted Serbia's Milan Gajic three minutes later when his volley from 25 metres beat the diving Djigui Diarra.
In the early semi-final, Brazil, who won two successive penalty shootouts to reach the last four, ended a 244-minute scoring drought in some style with three goals in the first 20 minutes to effectively wrap up their place in the final.
Brazil were 2-0 up in the first seven minutes with Anda Correa conceding an own goal after a Joao Pedro cross deflected off his leg before Guilherme doubled the advantage.
Boschilia put the game beyond any doubt in the 19th minute when Senegal goalkeeper Ibrahima Sy parried a cross into the midfielder's path before defender Jorge completed the first half scoring in the 35th minute.
Senegal, who had been unfortunate not to score when Sidy Sarr's 19th minute shot cannoned off the crossbar, were reduced to 10 men just before halftime when Elimane Cisse received a second booking.
With the match settled in the first half, the game meandered after the break with neither side creating any real chances until Guilherme put a gloss on the victory with his second goal in the 78th minute.
"We've had some good games and we've had some problems, but as a team we've grown through those difficult matches," Brazil coach Rogerio Micale said. "Today everyone played perfectly.
"I am very happy with my team as a whole. When no one scores against us that shows that our defence is working well and it has been a whole team effort."
(Reporting by Greg Stutchbury in Wellington; Editing by Nick Mulvenney/Amlan Chakraborty)
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