Martinez was a key player as River beat Boca Juniors to win the Copa Libertadores, scoring the clinching goal for his side in the second leg at the Santiago Bernabeu in Madrid.
The playmaker will now become the latest South American star at Atlanta, who appointed Frank de Boer as Gerardo Martino's replacement last month.
"The club has shown a lot of trust in me and I'm looking forward to working with Frank de Boer and my team-mates to continue making history at the club."
Vice president and technical director Carlos Bocanegra added: "We're excited to announce we've secured Gonzalo to a long-term contract with our club.
"Recently named as the best player in South America in 2018, Gonzalo is an attacking player who can play wide or centrally. His abilities complement our style of play and we expect him to make a smooth transition to MLS."
Martinez's signing creates a question surrounding Atlanta's roster as the attacker becomes the club's fourth designated player and MLS sides are only permitted to have three on their books.
He conquered Argentina.— Atlanta United FC (@ATLUTD) January 24, 2019
He conquered South America.
But he’s just getting started.
Welcome, Pity Martínez pic.twitter.com/2Dpe4tYxFj
Atlanta already boasted the likes of MLS MVP Josef Martinez, Miguel Almiron and Ezequiel Barco as their three designated players before adding the River Plate man.
The striker Martinez signed a new contract with the club in January after a record-breaking 2018 campaign, making him all but certain to remain with the MLS champions.
That leaves Barco and Almiron as the players who would seem the most likely candidates to depart.
Paraguay international Almiron, compared to Gareth Bale by Atlanta chief Darren Eales, has been seen as likely to move to Europe this winter, and has been linked with Premier League side Newcastle United.
However, the 19-year-old Barco had an up and down debut campaign in the league, scoring four goals and adding three assists in 26 games.
Reports in Argentina have linked Barco with a loan back to his old club Independiente, so he may be the choice to depart should Almiron remain through January.