The glamorous pair split up late last year after a three-year relationship. Brady, a two-time Super Bowl MVP, has since been seen with lingerie model Gisele Bundchen, and media outlets have reported the two are dating.
A Dec. 15 statement by Moynahan's publicist said Moynahan and Brady parted ways several weeks earlier.
On Monday, Moynahan's publicist, Christina Papadopoulos, said in a statement to The Associated Press that the actress "is over three months pregnant. Former boyfriend Tom Brady is the father."
"Privacy and consideration is appreciated at this time," the statement said. "No further comments will be made."
News of the pregnancy was first reported by the New York Post on Sunday. The Post quoted Papadopoulos as saying the actress was feeling "healthy and excited."
Messages left by The Associated Press with Brady's agent, Donald Yee, were not returned Monday.
Patriots spokesman Stacey James told the AP, "I think it would be inappropriate to comment."
Moynahan, 35, has appeared in films such as "Coyote Ugly," "I, Robot" and the ABC television series "Six Degrees." She grew up in Longmeadow, Mass.
Brady, 29, who has led the Patriots to three NFL titles, was named one of People magazine's "50 Most Beautiful People" in 2002.