The 33 year-old failed to convert a first-half spot-kick at the Allianz Riviera and hit the post in the build-up to Ousmane Dembele's late strike after Kylian Mbappe and Antoine Griezmann had put France on course for a routine win.
That was Benzema's third penalty miss in a row for his national side, having also failed to convert against Switzerland and Sweden in 2014.
However, on what was Benzema's first appearance for the world champions in five years and 237 days, the Real Madrid striker is pleased with how things went overall.
"There is a lot of pride and joy after that," he told TF1. "I had a good feeling going into the match after a good week of work and training. It's all about gaining momentum.
"It's been a difficult season with lots of matches. I feel good and that bodes well for the future.
"A match can often be like this with missed chances. The main thing is to create them and learn to do better next time."
Benzema may have endured a largely frustrating game in Nice, but he showed promising link-up play with goal-scorers Mbappe and Griezmann in a star-studded front three.
"We tried hard," he said. "It's not easy against teams that use five defenders and play with a low block. That is something we will have to work on in training.
"But overall it was a good match. We worked hard and that is the most important thing today."
Mbappe's breakthrough goal for France arrived seven minutes after Benzema's penalty miss, awarded for Neco Williams' handball in front of goal that also resulted in a red card for the Wales defender.
France looked comfortable from that point on, with Griezmann curling home a second goal early in the second period and substitute Dembele tapping in a third.
The front three of Griezmann, Benzema and Mbappe will be arguably the most feared at the upcoming Euro 2020 finals, and head coach Didier Deschamps is happy to give the trio "complete freedom" up top.
"Karim was unhappy not to score but he was always there," Deschamps told TF1. "A goal would have made both him happy, and me too, but there's no harm in keeping them for later.
"There is no fixed position for the three attackers. I give them complete freedom. Their profiles are complementary.
"Obviously when the ball is lost they know what needs to be done – they cannot disconnect from the others.
France's victory was their 19th in 24 matches and they now take on Bulgaria in their final friendly fixture ahead of facing Germany, Hungary and Portugal in a daunting Euro 2020 group.
"There's lots of good things to take out of this game," Deschamps said after seeing his side keep a third clean sheet in a row for the first time since October 2017.
"Obviously Wales had one less player and that made our jobs easier. We had lots of chances and it's good to conclude our first week together with this win. On another day the win could have been bigger, but it's a good start."