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Mali had been the overwhelming favourites but turned in an underwhelming performance, despite dominating possession and creating most of the chances.
Owono saved the final kick from Mali defender Falaye Sacko, although it was checked first by VAR to see whether he had advanced off his line before the kick was taken.
He had indeed moved forward but his back foot was still trailing on the line as Sacko took his penalty and the kick was allowed to stand by the referee, setting off tear-filled celebrations.
They had no real chances in the game, but never allowed Mali to get into any rhythm and proved difficult to break down.
Yet referee Bakary Gassama was encouraged to look again at his decision and, after consulting the pitchside VAR screen, changed his mind and overturned what had looked a soft penalty award.
As the game wore on, the clear-cut chances dwindled, with Mali making no progress into the Equatorial Guinea penalty area while the underdogs waited for rare opportunities on the counter attack.
"It's historic for us to get this far and it comes after excellent work by my players," said coach Juan Micha.
His Mali counterpart Mohamed Magassouba, whose country play in World Cup playoffs in March, said: "It's an incredible disappointment because it should not have even gone to penalties. We deserved more today."