Cora led Boston to the World Series title in 2018, when the Red Sox beat the Los Angeles Dodgers.
In making the announcement on Twitter, the Red Sox posted a picture of Cora lifting the Commissioner's Trophy with the words, "Welcome back, Alex Cora."
"I am grateful for the opportunity to manage once again and return to the game I have loved my entire life,” Cora said in a statement released by the team.
"I am eager to get back to work with our front office, coaches and especially our players. Boston is where I have always wanted to be, and I could not be more excited to help the Red Sox achieve our ultimate goal of winning in October."
Before arriving in Boston in his first stint as manager, Cora had been a well-liked bench coach with the Astros in 2017 when that team won it all, in a title that's now being called into question.
Houston was caught monitoring the opposing catchers' signals using a camera in center field of the team's stadium, Minute Maid Park, and then relaying that information to Astros hitters - often via someone banging on a trash can.
By knowing the upcoming pitch type, batters could adjust their timing. For instance, batters would know to swing early if a fastball was coming — or sit back and judge the location for a breaking ball or changeup.
The Red Sox were caught in similar acts in 2018, though MLB insisted that Boston's cheating "was far more limited in scope and impact" than the 2017 Houston Astros.
Boston was stripped of one draft choice for its 2018 misdeeds, and Cora stepped down in January.
Cora's rehiring comes a week after another key figure in the Astros scandal, then-manager AJ Hinch, also resurfaced. Hinch, who along with Astros General Manager Jeff Luhnow were fired when the scandal came to light, was hired last week as manager of the Detroit Tigers.