World champions France, who slumped to a 2-1 home loss to Denmark in their opening match, were without Kylian Mbappe and Karim Benzema at the start as coach Didier Deschamps made 10 changes to Friday's team.
Deschamps was back on the bench after he missed Friday's game against Denmark following the death of his father.
"We did good things considering all the changes. We were ahead and could have scored more but it's a pity we gifted them the equaliser," Deschamps, who insisted France's goal was to gear up for the World Cup, said.
"It was however a coherent performance. They barely threatened in the second half.
"The result is not satisfying and even if it's a competitive game our goal is to prepare for [the World Cup at] the end of the year."
Croatia were the most dangerous in a lively start before Nkunku was denied a goal for offside as France began to threaten on the break around the half hour mark.
France were rewarded for their good intentions in the 52nd minute when Rabiot collected a through ball from Wissam Ben Yedder and found the back of the net with a low shot for his second international goal.
Kramaric threatened again five minutes from time but Maignan pulled a decisive save to salvage a point.
France next travel Austria on Friday before hosting Croatia next Monday.