The World Cup winners and the European champions came into Saturday's 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 were without Kylian Mbappe due to 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 they 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.
What does it mean? Revenge at last
France have won the World Cup since losing the Euro 2016 final on home soil, but they had not beaten conquerors Portugal since that painful occasion.
Deservedly dumping Fernando Santos' side out of a tournament they won last time out would have been particularly satisfying – especially without Mbappe.
It will be Portugal's turn to seek a response as the teams meet once again in Group F at Euro 2020.
Griezmann the creator
In Mbappe's absence, many might have expected Griezmann to step up as France's chief goal threat. Instead, he was their creator.
The Barcelona forward had just one shot, which missed the target, but played three key passes. His gorgeous ball to Martial after 12 minutes deserved a better finish.
Patricio pays price
Although Portugal came into the match later in the second half – finishing with 18 attempts – they were outplayed before the break and relied on Patricio to come to their rescue time and again.
The Wolves goalkeeper made six saves but should have dealt with Rabiot's shot better, instead committing a costly error.