Returning to the starting line up for the first time since 2013, Brown Ideye opened scoring for the Nigerians before Kelechi Iheanacho scored his second in as many games and substitute Odion Ighalo put the encounter beyond the hosts.
Vincent Thill’s late goal was scant consolation for the hosts who struggled to match their more established opponents.
Coach Salisu Yusuf named six changes to the side that narrowly defeated Mali in Rouen last week as he brought on Ideye in place of Ighalo, goalkeeper Daniel Akpeyi for Carl Ikeme and Kenneth Omeruo for Leon Balogun.
Nigeria dominated proceedings with as much as 72 per cent of possession in the first half where they were rewarded with Ideye’s goal on 36 minutes as the striker pounced early after goalkeeper Anthony Moris had punched out Ogenyi Onazi’s shot from outside the box.
This came after key misses from Alex Iwobi and Aminu Umar who started in place of Moses Simon.
Both Iwobi and Umar made way early at the restart for Michael Babatunde and Simon as coach Luc Holtz also sent on Thill in place of Florian Bohnert.
The Super Eagles consolidated their lead on 69 minutes when Simon turned provider for Iheanacho to convert a simple tap in after Moris had been left stranded.
Yusuf made further changes as he brought on Gbenga Arokoyo for William Troost-Ekong in defence, Wilfried Ndidi and Raheem Lawal for Ogenyi Onazi and Shehu Abdullahi in midfield.
The hosts did not give up and would notch a goal on 90 minutes when Thill found the Nigerian defence open and shot past Akpeyi to wild celebrations on the field and in the bleacher stands.
Any hope of a final flourish by the hosts was dashed when Iheanacho created an opportunity for Ighalo to make it 3-1 in added-on time.
With two wins in their last two friendly matches, Nigeria will take confidence in their team building process ahead of the 2018 World Cup draws to be made in June.