The pair appeared together in Steven Spielberg's 1989 sequel Indiana Jones and the Last Crusade, with Sir Sean playing Ford's father Henry Jones.
"He was my father... not in life... but in Indy III," said Harrison in an interview with Variety.
"God we had fun - if he's in heaven, I hope they have golf courses. Rest in peace, dear friend," he added.
Ford recalled the "pleasure" of taking Sir Sean "for a ride in the sidecar of a Russian motorcycle, bouncing along a bumpy, twisty mountain trail and getting to watch him squirm".