Inter Milan winger Ivan Perisic opened the scoring for the home side in the 24th minute, with coach Zlatko Dalic's team up against England, the Czech Republic and Scotland at the Euros.
But a defensively-minded Armenia side made the most of a rare sortie into Croat territory when Colombian-born striker Wbeymar Angulo equalised in the 72nd minute.
Lazio striker Vedat Muriqi hit all four goals, including one penalty, as Kosovo outclassed San Marino 4-1.
Kosovo's neighbours North Macedonia came close to claiming the scalp of Slovenia after Napoli midfielder Elif Elmas scored the opening goal.
But home hearts were broken as Domen Crnigoj snatched an equaliser for Slovenia in the seventh minute of injury time.
North Macedonia are drawn with Austria, the Netherlands and Ukraine at the June 11-July 11 Euros.
Slovakia, in Group E alongside Poland, Spain and Sweden, were held to a 1-1 draw by Bulgaria.
In the only game pitching two Euro-bound sides against each other, the Poles played out a 1-1 draw against Russia, in Group B with Belgium, Denmark and Finland.
Jakub Swierczok got Poland on the scoresheet in the fourth minute before Russia pulled one back through Vyacheslav Karavaev 17 minutes later.