Six people died and five others were injured when gunmen opened fire on a packed bar in Loughinisland, County Down on June 18.
The shooting occurred during a troubled period in Northern Ireland's history where unionists, loyal to the governing British, clashed with nationalists who wanted a reunification of the partitioned island.
"What happened in Loughinisland in 1994 was an awful tragedy and deeply moving for all football fans," Football Association of Ireland Chairman John Delaney said in a statement on Thursday.
"I would like to thank UEFA for assisting us in commemorating this atrocity and take the opportunity to remember all those who lost their lives in the Troubles."
The commemoration was welcomed by the victims' families.
"The families are touched that this tragic event can be commemorated on such a poignant day, the 18th anniversary of the atrocity," said Niall Murphy, a solicitor representing the families.
