The 41-year-old actress says Cruise apologized in person Thursday.
"He came over to my house, and he gave me a heartfelt apology," Shields said Friday during an appearance on "The Tonight Show with Jay Leno." "And he apologized for bringing me into the whole thing and for everything that happened.
"And through it all, I was so impressed with how heartfelt it was. And I didn't feel at any time that I had to defend myself, nor did I feel that he was trying to convince me of anything other than the fact that he was deeply sorry. And I accepted it."
Cruise's spokesman confirmed the two celebrities had made up.
"It is true that his friendship with Ms. Shields has been mended," Cruise's spokesman, Arnold Robinson said in a statement. "He has not changed his position about antidepressants, which as evidenced by the black label warnings issued by the FDA on these types of drugs, are unhealthy."
Cruise and Shields had a public beef last year after the "Mission: Impossible III" star criticized her for taking antidepressants after the birth of her first daughter.
Cruise, echoing the position of Scientology, said in an appearance on NBC's "Today" show that depression can be treated with exercise and vitamins rather than drugs.
Shields, who wrote "Down Came the Rain: My Journey Through Postpartum Depression," has dismissed the actor's remarks as a "ridiculous rant" and "a disservice to mothers everywhere."
"I'm going to take a wild guess and say that Mr. Cruise has never suffered from postpartum depression," she wrote in an op-ed piece in The New York Times last year.
Cruise's mea culpa comes days after his company, Cruise/Wagner Productions, signed a with First & Goal LLC, an investment partnership headed by Washington Redskins owner Daniel Snyder.
Cruise/Wagner broke ties with Paramount Pictures last week in an unusually public dispute. Sumner Redstone, chairman of Paramount parent Viacom Inc., split with Cruise through an interview in the Wall Street Journal, saying the actor's public behavior, including jumping up and down on Oprah Winfrey's couch, and his aggressive defense of Scientology, alienated moviegoers and cost Paramount money at the box office.
Cruise's producing partner Paula Wagner slammed Redstone last week, calling his comments "surprising" and unbusinesslike. She said it was their decision not to renew their 14-year partnership with Paramount, choosing instead to follow a long-standing desire to make smaller, character-driven films on their own.