The substitute struck near the end to spare the blushes of Giovanni Trapattoni's men, who were second best throughout a drab contest played in Dublin
Substitute Simon Cox saved face for the hosts, scoring with three minutes to go to cancel out a second-half goal by Milan Baros in a performance that will not inspire much confidence in the Irish camp ahead of the summer tournament in Poland and Ukraine.
One plus for Giovanni Trapattoni, however, was the international debut of James McClean, with the in-form Sunderland man coming off the bench in the second half to a rapturous reception from the home support.
Both sides made a positive start to the game, but it was the Czechs who fired the first warning shot in the opening minutes after Jiri Stajner broke free and forced Shay Given to block low at his near post.
From there on, Ireland threatened with some enterprising play down the flanks, and should have been a goal up after a glorious chance was spurned by Robbie Keane with a quarter of an hour gone.
The Irish skipper did brilliantly to control a ball from defence with a deft touch inside the area, but his finish was rushed and blocked with relative ease by the legs of the onrushing Petr Cech.
The enthusiasm shown by both sides in the initial exchanges waned shortly after, with the game developing into an organized, if not imaginative contest in midfield.
On the stroke of first-half injury time, the visitors fashioned a rare chance with a snap shot by Jan Rezek that nicked off John O’Shea, but Given was able to get down quickly and parry as the match trickled into the break goalless.
However, the stalemate did not last long after the restart as a tidy finish by Baros in the 50th minute resulted in the opener. The former Liverpool man was picked out by Jan Rezek unmarked in the area, and put the ball past Given to give his side the lead.
Ireland were slow to respond, with the Czech Republic looking the better side as they continued to hold possession and play the match at their own pace as the second half wore on.
The hosts looked to be edging towards a demoralizing defeat, but found an equaliser out of nowhere with three minutes to go. Keith Andrews did well to win possession, and slipped for Cox, who finished from an acute angle to send the home fans into raptures.
Ireland finished the stronger, but did not find anything in the little time that remained, leaving Trapattoni with plenty to think about ahead of their next friendly against Bosnia and Herzegovina in Dublin on May 26th.
Michal Bilak meanwhile will look to build on a positive performance when the Czech Republic continue their Euro 2012 preparations with a visit from Hungary on June 1.