The Czechs looked like they had salvaged a draw when Tomas Rosicky’s long-range shot deflected into the net off a defender to level at 1-1 in the 70th minute.
But Gevorg Ghazaryan latched onto a pass deep in Czech territory in injury time and found the net with a shot that bounced off keeper Petr Cech and past a sprawling Michal Kadlec who was unable to clear his lines.
“We had a good start and a bad end,” Czech coach Michal Bilek told reporters.
The Czechs dominated possession but paid the price for squandering a clutch of quality chances in a match that highlighted the home side’s inability to finish.
Armenia took an early lead when a defensive error gave the visitors possession in front of the goal and Karlen Mkrtchyan’s fierce drive into the top corner gave a diving Cech no chance.