Nigeria came with a youthful side, with Odion Ighalo leading the attack alongside John Obi Mikel, Alex Iwobi and Victor Moses.
Inter Milan’s Ivan Perisic was the first to threaten as his shot from close range just slightly sailed over the top after being nicely set-up at the edge of the box.
The first blow eventually landed for them after a flying header from Mario Mandzukic diverted to Andrej Kramaric whose low shot got deflected into goal by a Nigeria's Oghenekaro Etebo.
On 39 minutes, Kramaric came close to adding a second following a cross from the left but his effort only found the top of the net, failing to trouble Francis Uzoho.
The second period started with a spate of corners falling to the Super Eagles of Nigeria. None of them proved to be of any meaningful fruition.
Buoyed by their halftime lead, Croatia were eager to continue from where they left off and Ante Rebic found himself in unfamiliar territory as he got on the end of a cross inside the box keen to profit.
Nigeria were given another blow as referee Sandro Ricci pointed to spot after William Ekong clattered on Mario Mandzukic in the 69th minute.
Captain and midfield sensation Luka Modric held his nerve and cool composure to send Uzoho the wrong way for the all-important three points.
The victory moves Croatia to the top of Group D, while the Super Eagles are bottom. Argentina and Iceland occupy second and third respectively.
Croatia: Subasic; Vrsaljko, Lovren, Vida, Strinic; Rakitić, Modric; Perisic, Mandzukic, Rebic; Kramaric.
Nigeria: Francis; Idowu, Ekong, Balogun, Shehu; Ndidi, Etebo; Iwobi, Obi Mikel, Moses; Ighalo.