Victor Wanyama started for Neil Lennon's men after joining up with the squad late following international duty, but the Hoops were stunned by Benjamin Hubner's fourth minute opener.
Hooper notched Celtic's first goal of their tour when he tapped home the opener in the 64th minute, and Stokes fired through the keeper's legs to wrap up victory in the 77th minute.
Motherwell were held to a 1-1 draw by Raith Rovers at Starks Park. Jamie Murphy put Well in front early in the second half, and Paddy Clark headed Raith's equaliser seven minutes from time.
Daniel Moore's eighth minute penalty gave Third Division Elgin a 1-0 win over Aberdeen, while SPL new boys Ross County were held to a goalless draw at Nairn County.