The deal is worth $26 million, according to multiple reports.
DeJong, 24, should serve as the Cardinals' everyday shortstop in 2018 after a rookie season in which he hit .285 with 25 home runs and 65 RBIs.
"Any time we make this kind of investment and commitment to a player, we want to do it with the right type of player," Cardinals vice president of baseball operations John Mozeliak said. "We talk a lot about the Cardinal Way and the character that we look at, and Paul exemplifies all of that."
The extension locks up DeJong past his arbitration-eligible years, which ran through 2020.
"It's a first-class organization and exactly where I want to be long term," DeJong said. "I think we're all pretty happy about this."
Over the past several years, the Cardinals have reached long-term deals with players just before the start of the regular season, including Stephen Piscotty, Allen Craig, Matt Carpenter and Kolten Wong.
The St. Louis Post-Dispatch first reported DeJong's extension agreement. FanRag Sports first reported the terms of the deal.
ESPN's Bradford Doolittle contributed to this report.