The Croatians were in control from the outset and took the lead on 32 minutes, when the unfortunate Oghenekaro Etebo diverted the ball into his own net.
Nigeria rarely threatened, and it was game over when Modric calmly tucked it away from the penalty spot after William Troost-Ekong inexplicably fouled Mario Mandzukic.
The win puts Zlatko Dalic's men two points clear of Argentina and Iceland, who played out a dramatic 1-1 draw earlier in the day.
One-sided from the beginning
'Vatreni' started the game on top but did not produce an attempt of any real significance until the 14th minute, when Ivan Perisic fired the ball a fraction over the crossbar following a lay-off from Mandzukic.
Andrej Kramaric went close soon after with an effort from distance, but instances of quality in the final third were few and far between.
When Croatia did take the lead on 32 minutes, it came through an own goal as Mandzukic's downward header from a corner was inadvertently bundled by in Etebo, who has recently joined Stoke City.
They then threatened to extend their margin, with Kramaric looping a decent header over the top after a superb ball-in from Ivan Rakitic and Sime Vrsaljko fluffing his lines after Mandzukic had played the ball into his path.
Nigeria, meanwhile, offered little going forward but came close to snatching an equaliser before the break as Arsenal's Alex Iwobi drove a cleared ball goalwards, only for Premier League rival Dejan Lovren to stick out a leg and block the shot.
Business-like Croats see the game out
Nigeria started the second period in more encouraging fashion: Leon Balogun saw a header deflected just wide under challenge from Ivan Perisic before Etebo fed Victor Moses with a driven diagonal ball and the Chelsea man dragged his effort wide.
Croatia, though, gradually reasserted their control and would have doubled their lead on 55 minutes but for a really poor miss from Ante Rebic, who volleyed wide from the inside the six-yard box after another great delivery from Rakitic.
Throughout the game, Nigeria's key players struggled to make an impact. Odion Ighalo's biggest contribution was a header directed straight at Danijel Subasic, while a frustrated Moses was lucky to escape caution as he repeatedly went to ground too easily.
20 minutes from time, the referee pointed to the spot after a blatant foul from Troost-Ekong, who wrapped his arms around Mandzukic and hauled him to the ground as he awaited a corner.
The ever-dependeable Modric calmly fired the ball into the bottom-left corner, sending the goalkeeper the wrong way and clinching an important three points.
Nigeria never really looked like forcing a grandstand finish, though Ivan Strinic did do well do hammer clear after substitute Kelechi Iheanacho cut the ball back towards Ahmed Musa.
It should, in truth, have been more comfortable for Croatia, but Matteo Kovacic failed to strengthen his claim for a starting spot as he slid a shot straight at the goalkeeper in stoppage time with Perisic demanding that the ball be squared.
Group C resumes on Thursday right with Croatia vs Argentina, followed by Nigeria vs Iceland on Friday afternoon.