The substitute's 102nd minute spot kick had enough power to find the net despite goalkeeper Kutman Kadyrbekov getting a hand on it and set up a last-eight meeting with holders Australia in a rematch of the 2015 semi-final.
After an early goal from Khamis Esmaeel was cancelled out by Kyrgyzstan's Mirlan Murzaev, it looked like Ali Mabkhout's 64th minute strike was going to settle the match for the hosts until Tursunali Rustamov's dramatic stoppage-time equaliser.
Alberto Zaccheroni's side know they will need to lift their game considerably to achieve their dream of winning the title back at the same stadium on Feb. 1 after making such heavy work of the hard-working but limited Asian Cup debutants.
A small 17,784 crowd turned out on an unusually cool evening in the Emirati capital but the vast Zayed Sports City arena was brought to life in the 14th minute when the hosts took the lead.
Ismail Matar swung a corner into the box, defender Khalifa Mubarak rose well to head the ball goalwards and Esmaeel nodded it home from close range.
Kyrgyzstan were level 12 minutes later when Akhlidin Israilov's pass put Murzaev through on goal and he took one touch to control the ball and another to take him past the keeper before slotting it into the net from a wide angle.
The Emiratis had struggled in front of goal throughout the group stage and the usually reliable Mabkhout headed wide from three metres a minute after halftime.
He made amends with his eighth Asian Cup goal after the hour mark, however, needing one touch to control Amer Abdulrahman's pass before rifling the ball into the net.
Kyrgyzstan defender Tamirlan Kozubaev should have equalised seven minutes later but somehow steered his shot wide from point-blank range although the Central Asians would not be denied and finally levelled from a stoppage-time corner.
Rustamov was gifted an extraordinary amount of space inside the six-yard box and the midfielder made no mistake with his header to send the match into extra time.
The home side made the brighter start to the extra period and the referee had no hesitation in pointing to the spot when Mabkhout fell under a challenge from Bekzhan Sagynbaev leaving Khalil to put away the penalty.
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Australia celebrate after Mathew Leckie scored the winning penalty against Uzbekistan. (Photo: AFC)
Maty Ryan was the hero for Australia as the defending champions edged through to the quarter-finals of the AFC Asian Cup UAE 2019 on Monday evening with a 4-2 win over Uzbekistan in a penalty shootout.
Ryan kept out spot-kicks from Islom Tukhtakhujaev and Dostonbek Khamdamov to leave Mathew Leckie to score the winning penalty that took Graham Arnold’s side into the next round of the competition.
Neither side had been able to find the back of the net during the previous 120 minutes, leaving Ryan to provide the heroics for his team, who now face the United Arab Emirates.
Takehiro Tomiyasu's lone strike sent Saudi Arabia crashing out of the Asian Cup as Japan beat the three-time champions 1-0 to reach the quarter-finals on Monday.
Tomiyasu's first-half header was enough to seal it for Japan as the last-16 game between two teams with seven titles between them failed to live up to its billing.
