The FIFA World Cup winner and the European champion came into Sunday's (AEDT) match tied on 10 points at the top of Group A3 through four matches, but the head-to-head primary tie-breaker made this clash pivotal after a goalless draw in France.
Kante's strike proved the difference as the Chelsea midfielder stepped up in the 53rd minute after the plethora of attacking talent at both ends had misfired.
France was without Kylian Mbappe because of a hamstring injury, but Anthony Martial might have had a first-half hat-trick and would have been relieved to see Kante come to his aid.
The first miss from the Manchester United forward came as he ran onto Antoine Griezmann's incisive pass but was quickly confronted by Rui Patricio, who had earlier saved comfortably from Kingsley Coman and this time blocked bravely.
France remained on top and Martial should have scored as he turned Adrien Rabiot's wayward acrobatic effort onto the crossbar from four yards, before Patricio made another sublime stop from a close-range attempt.
Fortunately for the visitors, Cristiano Ronaldo was similarly wasteful with a header over the top on the stroke of half-time.
It was Ronaldo's failing which would prove costly following the restart as Patricio spilled Rabiot's low shot and the unlikely figure of Kante pounced to prod into the net.
Jose Fonte directed an unmarked header onto the post as Portugal threatened a response, but that was as close as it came.
Ronaldo was unable to forge a first career goal against France to rescue his side, although he teed up Joao Moutinho for a powerful blast that drew an outstanding save from Hugo Lloris.
France plays Sweden next and Portugal visits Croatia in the final round of UEFA Nations League group games on Wednesday (AEDT), but the results are now largely academic.