Twenty countries from six confederations were entered in the esports event, with World Cup winners France represented by Corentin 'Maestro' Thullier and Lucas 'DaXe' Cuillerier.
The players wore national team jerseys as they competed on PlayStation and XBox with both one-on-one FIFA 19 matches and two v two.
Teams were divided into four groups of five before the knock-out stage.
"DaXe and I had some really tough matches over the two days so to come away as champions and the title of the best eFootball nation in the world is really special," said Thullier, the world number six on the PS4 platform.
Christian Volk, FIFA's Director of eFootball and Gaming, said the eNations Cup was another step in the professionalisation of the virtual game.
"The FIFA eNations Cup has presented an important stepping stone to further grow the eFootball ecosystem, offering member associations with the chance to run their own national selection process and qualifying events," he added.
Last year's FIFA eWorld Cup winner Mosaad 'MsDossary7' Aldossary was competing for the Saudi Arabian team in the eNations Cup and was beaten by Thullier in the opening day's round of games.
The winning French players also won 1,500 FIFA 19 Global Series points that go towards qualification for this year's FIFA eWorld Cup.
The top 60 competitors on the final EA SPORTS FIFA 19 Global Series points leaderboard qualify for the Global Series Playoffs in June. The best 32 then go on to the FIFA eWorld Cup finals.
(Reporting by Alan Baldwin, editing by Pritha Sarkar)