Eyeing their first World Cup berth since 2006, the Czechs now face Denmark in the play-off final in Prague on March 31 for a ticket to the tournament hosted by the United States, Canada and Mexico.
Ireland raced into a 2-0 lead in the first half but the Czechs eventually pulled one back with a penalty then equalised just five minutes from time.
After a tense extra-time the Czechs then converted four penalties to Ireland’s three in the shootout.
Troy Parrott opened the scores for Ireland from the spot, beating Kovar at his right post 19 minutes into the game for his sixth goal in this qualifying campaign.
The penalty was awarded following a delayed VAR review of a foul on Ireland skipper Nathan Collins in the Czech box three minutes earlier.
Ireland went two goals up four minutes later when Dara O’Shea headed a corner towards the Czech goal and a disoriented Kovar shoved the ball into the net after a series of deflections.
Patrik Schick brought the hosts within a goal from the spot against the run of play in the 27th minute after Ryan Manning had pulled Czech skipper Ladislav Krejci down in the box.
The Czechs looked toothless for most of the second half, but Krejci headed home from a corner five minutes from time, taking the game into a goalless extra time.
Parrott, Adam Idah and Robbie Brady converted their penalties while Finn Azaz and Alan Browne were denied by Kovar.
Krejci, Tomas Soucek, Patrik Schick and Jan Kliment scored for the hosts in the shootout, with Mojmir Chytil’s poor shot stopped by Caoimhin Kelleher.
Ireland will bemoan wasted chances as Collins and Jayson Molumby hit the woodwork and Parrott was narrowly denied by a diving Kovar with an 80th-minute header.
The Czechs have made amends for a lacklustre qualification during which they swapped coaches just before the play-offs amid mounting criticism from fans and pundits.
On Wednesday, Czech police said they had charged 32 people in a massive crackdown on a match-fixing network, the second such case in less than a decade.
Long-time skipper Soucek lost the captain’s band before the game after a fumbled attempt to console fans dismayed with the qualifying performance last autumn.
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