Hendricks (1-1) struck out seven with no walks. Only one Padres baserunner advanced to second base.
Hendricks came in with six no-decisions in seven starts, including one against San Diego at Wrigley Field on April 18.
Bryant homered to straightaway center field on the seventh pitch of the game by Odrisamer Despaigne. Dexter Fowler was aboard on a walk for Bryant's fifth homer.
Bryant made his big league debut on April 17 against the Padres at Wrigley Field. He starred at the University of San Diego before the Cubs took him with the second pick overall in the 2013 amateur draft.