The Eagles enjoyed the better of normal time in Limbe, but the game finished 0-0 after extra time and Owono’s save from defender Falaye Sacko clinched a 6-5 victory on penalties with Senegal awaiting his side in the quarter-finals.
Defensive midfielder Amadou Haidara might have given Mali a 32nd-minute lead, but scuffed his shot as he fell after controlling the ball deep inside the penalty area.
Their frustration grew when they were awarded a 40th-minute penalty for Josete Miranda’s challenge on Moussa Doumbia, only for referee Bakary Gassama to change his decision after being advised to review the incident by the VAR official.
Mohamed Camara passed up a glorious opportunity to put Mali ahead when he fired wildly over from Yves Bissouma’s 58th-minute cut-back and substitute Moussa Djenepo saw his effort deflected just wide with 19 minutes remaining.
Equatorial Guinea enjoyed their best spell of the game as normal time drew to a close, and they carried that into extra time with Basilio Ndong testing Mounkoro with a long-range strike which bounced just in front of him, but it was they who held their nerve from 12 yards.
AFCON 2021 quarter-final fixtures and results
Saturday January 29
Quarter-final 1: Cameroon vs Gambia, 4pm (Japoma Stadium, Douala) – Live on Sky Sports
Quarter-final 2: Burkina Faso vs Tunisia, 7pm (Roumde Adjia Stadium, Garoua) – Live on Sky Sports Premier League
Sunday January 30
Quarter-final 3: Round-of-16 game 7 winner vs Round-of-16 game 6 winner, 4pm (Olembe Stadium, Yaounde) – Live on Sky Sports Premier League
Quarter-final 4: Round-of-16 game 5 winner vs Round-of-16 game 8 winner, 7pm (Japoma Stadium, Douala) – Live on Sky Sports Football