An inspired Patricio kept France at bay until he was unable to properly deal with Rabiot's low angled strike early in the second half, pushing it straight to Kante who forced home from inside the six-yard box.
Anthony Martial missed three clear-cut first half chances for France before Kante scored only his second global goal in the 54th minute, and his first since 2016, to end Portugal's run of five successive clean sheets.
France sit top of their Nations League group after their win in Portugal and have picked up 13 points from their five games so far, three points more than the Portuguese. The first two were saved by Portugal goalkeeper Rui Patricio while Martial hit the crossbar with a header. It was only Portugal's second defeat since the 2018 World Cup.
"We deserved the win and we have fulfilled our objective of finishing top". I'm very proud of the players.
With victory for either country enough to win the group, Deschamps made two changes to the team that drew 0-0 with Portugal at the Stade de France last month.
"I don't know what went wrong in the first half, it wasn't what I expected but it was my responsibility", said Portugal coach Fernando Santos.
"We were better in the second half but then conceded the goal which settled the game... we had three or four chances to equalise".
Portugal's Cristiano Ronaldo is just seven goals shy of the men's national team record held by former Iran striker Ali Daei with his 109 goals. He missed a free-kick from close quarters and could not score.
The Portugal captain was back in the Seleccao lineup against the world champions but had been left frustrated due to the shortage of clear-cut opportunities.
The Portugal captain has now gone almost 450 minutes without scoring against Les Blues, a poor record for somebody of the stature. Portugal had beaten Netherlands to win the inaugural UEFA Nations League title a year ago but won't be part of the knockouts this time. But for now, Ronaldo needs to focus on the following game for Portugal.