It marks the first time Hartley has been dropped by Jones, but the Australian insisted that, as long as his disciplinary record remains clean with Northampton Saints beforehand, the 31-year-old will lead England in their bid for a third successive Six Nations title.
But against Samoa, George Ford and Chris Robshaw will serve as co-captains, with England hoping to claim their 200th win at Twickenham on Saturday.
"We want to test our ability, if Dylan's not available, to put a team on the field and have leadership density," Jones said.