The '99 Problems' rapper will stand in for the Beastie Boys, who were forced to pull their slot at the event after Adam Yauch was diagnosed with cancer.
The Beastie Boys have also postponed the release of their new LP Hot Sauce Committee while Yauch is treated.
Jay-Z performed festivals in Europe last year, headlining at Glastonbury, Wireless and Roskilde, but this will be his first American date. Other performers at All Points West include Coldplay and Tool. Jay-Z tops the bill on July 31.