The Northampton hooker has been a key figure since Jones took charge, having been handed the captaincy, but has found his spot in the team come under increasing pressure from Saracens' Jamie George.
George, who started all three Tests for the British & Irish Lions against New Zealand in the summer, will make his first start for England after Jones took the decision to bench Hartley.
George's inclusion is one of nine changes made by the Red Rose coach from the win over Australia last week, with Exeter No.8 Sam Simmonds winning his first start in the back-row, replacing the injured Nathan Hughes.
Owen Farrell is rested so Alex Lozowski is named at centre, partnering Henry Slade in midfield, while Maro Itoje returns to the starting line-up at blindside flanker.
Scrum-half Danny Care gets his first start of the autumn while loosehead prop Ellis Genge and lock Charlie Ewels are also drafted into the team for the Twickenham Test match.
"This is an exciting squad to play against Samoa and we are expecting them to be immensely physical and committed this weekend," said Jones.
"We want to follow up last week's performance against Australia and play better again this week. Our intent in every game and every training session is to be better.
"This week it is an opportunity for some squad members who haven't been playing to put their best foot forward. We will have to play smart and will need to find ways to win the contest against Samoa."
England: 15 Mike Brown, 14 Jonny May, 13 Henry Slade, 12 Alex Lozowski, 11 Elliot Daly, 10 George Ford (co-capt), 9 Danny Care; 1 Ellis Genge, 2 Jamie George, 3 Dan Cole, 4 Joe Launchbury, 5 Charlie Ewels, 6 Maro Itoje, 7 Chris Robshaw (co-capt), 8 Sam Simmonds.
Replacements: 16 Dylan Hartley, 17 Joe Marler, 18 Harry Williams, 19 Nick Isiekwe, 20 Courtney Lawes, 21 Ben Youngs, 22 Piers Francis, 23 Semesa Rokoduguni.