People.com reported the couple went their separate ways about two weeks ago, but their representatives denied the account at the time.
E! News Tuesday cited unnamed insiders as confirming the report is true, however. The program also noted on its Web site that Witherspoon and Gyllenhaal's publicists are now declining to comment on the story.
"They needed time to figure it out and they were on different coasts," a source told E! News. "When they were finally together, they talked it out and decided they're not going to be together anymore."
"There are no other people involved," another insider added. "The relationship just ended. It just fizzled. But they also wanted to be careful and private about it because of Reese's kids."
Witherspoon was previously married to actor Ryan Phillippe, the father of her two children.