The Northampton number eight takes over the reins from Test skipper Chris Robshaw, who leads Harlequins against Leicester in the Premiership final the previous day.
Dowson has been a senior figure in Stuart Lancaster's England squad, even after losing his place in the starting side to Ben Morgan during the Six Nations.
With Morgan recovering from a hamstring injury, Dowson will start against a star-studded Barbarians side and he has been chosen as captain ahead of his club skipper Dylan Hartley.
"Phil is one of the key members of our leadership group. He will captain the team on Sunday," said England forwards coach Graham Rowntree.
Hartley is set to play his first game since the Six Nations after serving an eight-week ban for biting Ireland flanker Stephen Ferris.
Rowntree believes Hartley is a future England captain but this weekend wanted the Northampton hooker to concentrate on his scrummaging.
"The fact he has been out for eight weeks, I want Dylan to focus on playing, to focus on his game and not be saddled with captaincy issues," Rowntree said.
Dowson's elevation is a reward for his leadership during the Six Nations as a new-look England team defied the odds to finish second in the championship.