Germany were much the better side in the first half at the Stade de France and had a deserved lead at the break thanks to Toni Kroos' penalty.
Joachim Low's side could have had a more comprehensive lead at half-time were it not for the work of Hugo Lloris, and France ultimately fought back with a second-half improvement.
Antoine Griezmann got the equaliser with a fine glancing header, before sealing the win late on with a contentious penalty – Mats Hummels' foot was trodden on by Matuidi as he attempted to make a sliding challenge.
Nevertheless, Matuidi is convinced France deserved it and paid tribute to Deschamps' half-time talk and adjustments as the reason for Les Bleus' turnaround.
"We spoke at half-time," the Juventus midfielder told M6. "The coach told us what he had to say and so did we [the players].
"The coach was very good tactically and we were better in the second half with a three-man midfield.
"We played better without the ball and they started losing their grip too after we equalised. It's about confidence. They [Germany] lack it right now and we have plenty of it."
The victory takes France up to seven point in Group 1, meaning they only need a draw against the Netherlands next month to ensure finishing top of the trio of teams.