The United States defender, who was on loan at Atlas this season, had been in Mexico since leaving the LA Galaxy for Pachuca in January of 2016.
The 30-year-old was signed using Targeted Allocation Money (TAM) and will be officially added to the roster once the transfer window re-opens on July 9.
Gonzalez won a domestic title and the 2016-17 CONCACAF Champions League with Pachuca. Prior to his move to Mexico, Gonzalez played for the Galaxy from 2009-15, where he won three MLS Cup titles.
"Omar has won numerous championships and has played on the biggest stage in world football," said TFC general manager Ali Curtis in a team statement. "He is an experienced defender with over 200 appearances in MLS, including 25 playoff matches where he won five trophies in seven years
"His experience as a player but equally as important, who he is as a person will be a welcomed addition to our group here in Toronto."
Gonzalez has made 49 appearances for the U.S., and was part of the squad at the 2014 World Cup in Brazil. He had an own goal in the infamous 2-1 defeat to Trinidad & Tobago that eliminated the U.S. from qualifying for the 2018 World Cup.