Joyner will assist new hitting coach Steve Henderson. The Phillies reshuffled their coaching staff after finishing 81-81 following five straight division titles.
He previously was the batting coach for San Diego during parts of the 2007 and 2008 seasons.
The 50-year-old Joyner was a left-handed hitting first baseman for 16 seasons with four teams. He finished his career with a .289 batting average, 409 doubles, 204 home runs and 1,106 RBIs in 2,033 games.