Rumours of a possible break-up emerged online overnight and Kelly's spokesperson has now confirmed to People that the couple recently separated.
A source close to both Kelly and Jeter insisted that the two remain on good terms, saying: "They care about each other and [the split] was amicable. They're still friends."
Kelly first began dating Jeter in 2008 and has often been seen cheering him on during baseball games at Yankee Stadium.
Prior to his relationship with Kelly, Jeter had been linked to Mariah Carey, Jessica Biel and Jordana Brewster.
Kelly will next star in Charlie's Angels, which premieres on Thursday, September 22 at 8/7c on ABC and will air on E4 in the UK.
> Minka Kelly: 'I have a lot in common with Charlie's Angels character'
> Minka Kelly teases Charlie's Angels role
Watch Minka Kelly's emotional reaction when Derek Jeter achieves his 3,000th career hit below: