Now 28 Rafael arrived in Manchester in 2008 when Alex Ferguson brought the Da Silva twins Rafael and Fabio to Old Trafford where they helped United to three Premier League titles.
Since arriving at Lyon on a four-year deal in 2015 Rafael has played 117 games for Lyon, 25 of them in European competition.
The club said Monday they were "delighted with Rafael's loyalty to the Lyon jersey" publishing a picture of the right-back holding up a Lyon shirt bearing his name and the number 2021, until when his contract runs.
"Everybody knew I wanted to stay here. It's a club and a city that I really like," the player said.
"I've been trying to show on the pitch this desire to stay and we reached a two-year agreement," he said.
His brother Fabio is also in France where he plays for rival Ligue 1 outfit Nantes.