Wales debutant Nathan Broadhead secured a stunning 1-1 draw for Robert Page’s side as they scored with their only shot on target in Split.
Andrej Kramaric’s sweetly struck shot on 28 minutes gave the hosts a deserved half-time lead.
Wales improved after the interval and might have levelled on the hour, but Dan James’ volley missed the target.
Ivan Perisic hit the bar as Croatia sought a second, but Broadhead levelled from close range in injury-time.
The goal, after a long throw caused chaos in the Croatian penalty area, came totally against the run of play, but Wales will not care a jot after securing an unexpected point.
Croatia had won 34 and drawn one home European qualifier in their history.
But Wales upset the odds in the third minute of added time through Broadhead, who plays in League One for Ipswich Town.
