The United States men's national team center-back, who has been on loan at Atlas from Pachuca, agreed to an initial contract until the end of the 2021 Major League Soccer season with the option of an additional year, according to TSN's Kristian Jack.
The 30-year-old will be added to the TFC roster on July 9.
"Omar has won numerous championships and has played on the biggest stage in world football. He is an experienced defender with over 200 appearances in MLS, including 25 playoff matches where he won five trophies in seven years," Toronto FC general manager Ali Curtis said.
"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 was apparently described to Jack as a "cornerstone" of Greg Vanney's defense going forward. The Texan made his professional debut with the LA Galaxy in 2009 after being picked third in that year's SuperDraft, and subsequently won three MLS Cups and two Supporters' Shields with the Californian outfit.
Gonzalez became the first American defender to sign an MLS Designated Player deal in August 2013 but moved to Liga MX in late 2015.
In addition to his two Gold Cup triumphs with the USMNT, Gonzalez won the 2016 Clausura and the 2016-17 CONCACAF Champions League with Pachuca.