The Socceroos star will link up with fellow Australians Brandon Borrello (Dynamo Dresden) and John Iredale (Paderborn) in the German second division having signed on a free transfer.
Irvine made 21 appearances for Hibernian last season, with three assists and one goal.
"I'm delighted to be here," Irvine said. "The club and its values are a perfect fit for me. The way St. Pauli play football suits me, too. I can't wait to meet my teammates now and get started."
Irvine's first appearance could be an 18 July trial match against Mathew Leckie's former club, Hertha BSC. The season proper begins at home to Holstein Kiel a week later.
His first match-up against St Pauli's fierce city rival, SV Hamburger will come on 15 August, followed by a visit to Iredale's Paderborn on 22 August.
"Jackson Irvine gives us more flexibility in midfield because he can play both an attacking and a defensive role," St Pauli manager Timo Schultz said. "He also brings a certain physicality and rugged style of play that will add stability, and his experience will benefit our younger players."
Irvine-old previously spent three years with the English Championship side Hull City, where he made 112 competitive appearances (10 goals, 9 assists).
He made his Australia debut in 2013 and has scored five goals and provided seven assists in 36 appearances to date.