Not for the first time in the tournament, the substitute was his team's hero, with Saponjic's strike settling an enthralling and evenly contested match that had been punctuated by goals from Andrija Zivkovic and Youssouf Kone.
Serbia returned to the scene of its quarter-final win over USA.
It took the Serbs just four minutes to take a deserved early lead when lively Zivkovic was allowed time and space to run through on goal and pick his spot with a low left-footed shot into the corner after Souleymane Coulibaly had failed in his attempts to cut out Nemanja Maksimovic's threaded through pass.
Serbia should have gone two in front nine minutes later but having been caught out for the goal Coulibaly was able to come to Mali's rescue, clearing off the line with his keeper stranded after Stanisa Mandic had cut the ball back for Sergei Milinkovic's to strike at goal.
The Africans had another near escape when Serbia again cut through its ranks easily, with Zivkovic and Malin Gajic combining well on the right to set up Stanisa Mandic. But while the latter's low cross found Serbia's No 9 just five metres out, his touch was too faint and the ball flicked off his right boot and wide of the far post.
Serbia was on top and no-one could have envisaged Mali levelling matters. The goal came out of nothing, with Youssouf Kone gathering possession in an unthreatening position on the left, over 30 metres from goal, and stunning everyone - not least keeper Predrag Rajkovic - with a ferociously struck left-foot shot that skidded into the bottom-right corner.
Mali, having been hanging on, suddenly looked the more likely winners. This continues at the start of the second half, with Diadie Samassekou playing in Diedonne Gbakle only for the latter to hesitate at the crucial moment, allowing Rajkovic to narrow the angle and block from his weakly struck shot.
Serbia was struggling at the other end but, with 18 minutes remaining, a moment of pure inspiration nearly settled the game in its favour. Gajic was the player who supplied it, controlling a dropping ball on his instep 30 metres from goal and crashing in a superb dipping volley. Sadly for the midfielder, the ball bounced off the crossbar and landed a couple of centimetres in front of the line.
That left extra time to settle the outcome and Saponjic to steal the headlines. The forward had come off the bench to become Serbia's hero in the last 16 against Hungary and he was their super sub again, scoring the goal that took his team through to a historic final.
Zivkovic again played his part with a flighted corner and when Milos Veljkovic rose highest to knock the ball back across goal, Saponjic was on hand to nod the ball home.
