Croatia were in control for much of the game and took a deserved lead into the interval before Luka Modric tucked home a second-half penalty to wrap up three crucial early points in the tournament.
There was an element of fortune about the opening goal as Mario Mandzukic’s header was deflected into his own net by Oghenekaro Etebo after 32 minutes, but it was the least Croatia deserved as the Super Eagles failed to rise to the occasion.
Nigeria offered little of note going forward, with Chelsea’s Victor Moses resorting to a number of theatrical falls while Alex Iwobi was taken off after a silent hour of football for the Arsenal playmaker.
Croatia kept pressing for another goal to make the game safe, and they got their reward from the spot-kick after Ekong bizarrely wrestled Mandzukic to the floor at a corner with 19 minutes remaining.
Nigeria were furious with referee Sandro Ricci as the Brazilian booked Ekong for good measure, but it was the correct decision before Modric calmly slotted the penalty home to seal the win.