In a winner-takes-all contest in Lisbon, the world champions prevailed 1-0 thanks N'Golo Kante's second-half strike, advancing due to their superior head-to-head record over Saturday's opponents.
Although Portugal - the Nations League holders who will not now defend their title - piled on the pressure in the closing stages, it was a deserved success for France.
Les Bleus had sensationally lost 2-0 to Finland in a friendly earlier in the week, but a much-changed side could have been out of sight before half-time against Portugal.
Rui Patricio was in inspired form in the home goal, although one of his six saves eventually succeeded only in teeing up Kante's decisive goal, leaving Varane to reflect on a standout victory.
"We are very happy with the victory - the way we got it, too," Varane told TF1.
"We saw a lot of solidarity and the state of mind was great. We created great opportunities but were also very solid. Portugal were strong on set-pieces.
"Over the next few months, this will be our benchmark match.
"We saw a lot of good things, we managed to combine well, to work together in defense. We will be able to rely on that to project ourselves towards the next objectives."
While Antoine Griezmann was the star in attack - creating three chances, including the Adrien Rabiot shot Patricio spilled - Varane and his defensive colleagues performed admirably at the other end.
Portugal had 18 shots but only one of Hugo Lloris' six saves truly tested the France captain, while Cristiano Ronaldo hit the target with just one of his half-dozen attempts.
Varane led the way with six clearances ahead of center-back partner Presnel Kimpembe's four, including one sublime header in front of Ronaldo 13 minutes from time, as Portugal sent in 18 open-play crosses.
Watching on from the touchline, coach Didier Deschamps agreed it was a performance France could use as an example moving forward.
"Taking into account the quality of the opponent as well, of course," he said.