The rock veterans announced the move on Monday as they prepared for the start of a two-year world tour, beginning in the US in September.
The group lost control of much of its famous catalogue to former manager Allen Klein in the early 1970s and has been unable to release a single retrospective album since then.
Forty Licks, set for release on 30 September in most of the world and a day later in the US, will be a two-CD set ranging from early 1960s classics such as (I Can't Get No) Satisfaction to recent hits and four new, unreleased tracks.
Mr Klein, who was also briefly The Beatles' manager, said that the Rolling Stones' lead singer, Sir Mick Jagger, had asked the companies to work together for the sake of the new album.
"Mick asked that we should try to square the circle - The Stones wanted it and I'm happy we could do it with them," said Mr Klein in a statement.
The collection will bridge the gap between the tracks controlled by Allen Klein's ABKCO Records and the current Rolling Stones label, Virgin - part of the EMI group.
Only one of the album's four new tracks has been named - Don't Stop, which will be release as a single later this month.
ABKCO is also to release digitally remastered versions of 22 Rolling Stones albums, including some that have long been unavailable on CD, such as the UK versions of 1965's Out of Our Heads and 1967's Between the Buttons.
The reissues, distributed through Universal Music, will be released on 20 August.
The Rolling Stones, who had their first hit in 1963 with a version of The Beatles' I Wanna Be Your Man, begin their North American tour at Boston's Fleet Center on 3 September.
They will visit Europe and Australia in 2003 and have been in discussions over whether to take the tour to China for the first time.