The French defender was an important part of the Timbers back line in 2013 before a knee injury ended his season prematurely.
Silvestre, 36, made eight league appearances for the Timbers in 2013, before tearing his ACL on May 2 and missing the rest of the season.
In a club release, the former Manchester United and Arsenal defender said he is set to stay in the Pacific Northwest, which likely means his career will come to a close after 17 professional seasons.
“I loved my time with the Timbers,” Silvestre said. “My family and I have enjoyed our time in Oregon and we plan to stay here for the foreseeable future. I am excited to stay and seek other opportunities."