Nigeria's Oghenekaro Etebo was credited with the own goal as Croatia broke the deadlock just after the half-hour mark at the Kaliningrad Stadium.
A diving header from Mario Mandzukic took a deflection off the Nigerian midfielder and crept into the goal for a deserved lead as Croatia dominated the count of chances created in the first 45 minutes.
Nigeria offered little more after the break and were dealt a second setback after William Troost-Ekong was whistled for grabbing and impeding Mandzukic while defending a corner.
Luka Modric converted from the spot to double Croatia's lead with their only shot on target before Mateo Kovacic's attempt in stoppage time.
But they didn't have to do much more as Nigeria, despite bringing on Ahmed Musa, Kelechi Iheanacho and Simeon Nwankwo off the bench, only forced Croatia keeper Danijel Subasic to make two save.