Regular co-captains Dylan Hartley and Owen Farrell are named among the replacements as Jones gives a chance to some of his squad players in a bid to replicate next year's World Cup when England start with two games in four days.
Cokanasiga, the 18 stone Fiji-born back, turned 21 on Thursday. He will play on the right wing, with Chris Ashton, who scored a try after two minutes against the All Blacks, switching to the left.
Jack Nowell and Alex Lozowski form a new centre pairing while scrumhalf Danny Care gets his first start since last year's Six Nations, with Richard Wigglesworth on the bench.
Alec Hepburn, Harry Williams and hooker Jamie George provide a completely new front row, with Charlie Ewels and Maro Itoje at lock.
Courtney Lawes will play blindside flanker with Mark Wilson switching from number eight to openside and Zach Mercer making his first start, at the back of the scrum.
Uncapped 19-year-old Worcester flanker Ted Hill was named among the replacements.
Jones has tried to use this week as a dry run for next year’s World Cup, when England open up against Tonga and face the United States four days later.
He has said he plans to play his strongest team in the first match then try to use more squad players against the Americans, resting some of his big names for the tough encounters to come against Argentina and France.
"This is a good opportunity for us to test the depth of the squad," said the Australian, who completes England's November campaign against his homeland next week.
"A number of players have changed their roles going from finishers to starters and starters to finishers so that is the essential change to the squad.
"It is exciting to be able to give starting opportunities to Zach Mercer and Joe Cokanasiga and young Ted Hill on the bench.
"We took Joe on tour in 2017 to Argentina. He was a young lad, probably didn’t really understand what it takes to be a top line player but he had a lot of natural talent. Now he's starting to hone that talent through hard work, and with a real growth mindset, so we're really pleased with how he’s progressed.
"We have tested ourselves in having a shorter preparation. We gave the players two days off after three weeks of intensive work. We have had a short preparation but a good preparation.”
Jones’s bid to get his players into a Japan mindset extended to him giving his squad chopsticks to eat their sushi on Tuesday as they re-convened at their usual Surrey base.
It is the second time England have faced Japan, the other coming in the 1987 World Cup pool stage when England triumphed 60-7.
The current side are a far-different proposition from those amateur days but are struggling to reach the heights of the 2015 World Cup when, led by Jones, they stunned South Africa in the pool phase.
"We are expecting plenty of energy, aggression and fast ball movement," he said of his former charges, now coached by former All Black flanker Jamie Joseph.
"They will be full of surprises, quick taps, lineouts and plays. They are going to have a bag of magic."
England team to play Japan
15 Elliot Daly (Wasps, 23 caps)14 Joe Cokanasiga (Bath Rugby, uncapped)13 Jack Nowell (Exeter Chiefs, 28 caps)12 Alex Lozowski (Saracens, 4 caps)11 Chris Ashton (Sale Sharks, 41 caps)10 George Ford (Leicester Tigers, 49 caps) captain9 Danny Care (Harlequins, 83 caps) 1 Alec Hepburn (Exeter Chiefs, 4 caps)2 Jamie George (Saracens, 30 caps)3 Harry Williams (Exeter Chiefs, 13 caps)4 Charlie Ewels (Bath Rugby, 8 caps)5 Maro Itoje (Saracens, 24 caps) vice-captain6 Courtney Lawes (Northampton Saints, 66 caps)7 Mark Wilson (Newcastle Falcons, 6 caps)8 Zach Mercer (Bath Rugby, 1 cap) Replacements16 Dylan Hartley (Northampton Saints, 95 caps)17 Ben Moon (Exeter Chiefs, 2 caps)18 Kyle Sinckler (Harlequins, 15 caps)19 Ted Hill (Worcester Warriors, uncapped)20 Sam Underhill (Bath Rugby, 7 caps)21 Richard Wigglesworth (Saracens, 31 caps)22 Owen Farrell (Saracens, 63 caps)23 Henry Slade (Exeter Chiefs, 15 caps)
(Reporting by Mitch Phillips, editing by Toby Davis)
