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 its 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.
"So, it's an opportunity for these guys to show it. Dylan understands it's about developing a team for the World Cup.
"So, it's not about making anyone uncomfortable. We know he's a great captain and we know he can do a great job for us. But this is an opportunity for the rest of the squad to show they can step up.
"There's no decision on the World Cup. The only decision we've made is that, all things being equal, and he doesn't have one of those 'mystical' experiences at Franklin’s Gardens, that he'll be captain for the Six Nations."
Asked about the decision to have Ford captain the backs and Robshaw the forwards, Jones replied: "Why not? You could have three captains. I've had a team that's had four vice-captains.
"Just because the tradition is that you have one captain, it doesn't mean that you have to have one captain. There's nothing that says you have to have one captain."