In addition to the six changes in the starting line-up there are two positional switches, but this selection also means the coach has been able to pick four players - Colin Charvis, Dafydd Jones, Michael Owen and Gavin Henson - to start every match in the Lloyds TSB Autumn Series.
There are also a further four players who faced South Africa in the first Test of the series, Hal Luscombe, Shane Williams, Brent Cockbain and Duncan Jones, meaning Ruddock has plumped for a strong line-up against the Cherry Blossoms.
Scrum half Gareth Cooper has been handed the chance to impress his coach with Dwayne Peel moving to the bench, but the Wales coach has, wherever possible, kept faith with the squad that got within two points of the Springboks and within a point of an historic victory over the All Blacks.
Rhys Williams comes in at full back for Thomas and Ceri Sweeney renews his regional half back partnership with Cooper in the absence of Jones.
An injury to Sonny Parker's wrist means he misses the game and Hal Luscombe has returned from his knee injury to take up a position on the wing, with an injury audit in place to consider the final position on the bench. It's the versatile Tom Shanklin that leaves the wing to fill in for Parker at outside centre.
In the forwards Jonathan Thomas returns to the second row in place of Llewellyn and props Duncan Jones and Gethin Jenkins both start where they finished off against the All Blacks in the front row, with Adam Jones moving to the bench to make way for namesake Duncan in the starting line-up.
On the bench Kevin Morgan gets his first taste of international duty since injuring his ankle in last season's RBS Six Nations Championship to cover wing and full-back.
Ryan Jones will undergo a fitness test on Thursday and if he fails that Alix Popham will take his place on the bench. "We've said all along that we are looking for continuity in both selection and performance through out the Lloyds TSB Autumn Series and the final Test against Japan is no exception," said Ruddock.
"One of our goals was to create cohesion in the team and in the squad as we build to all the RBS Six Nations.
"Ceri Sweeney, Gareth Cooper and Johnathon Thomas are the only players being given their first start in the series and each of them have played a significant part in the squad preparations as well as on matchday from the bench.
"That's a testament to the high value we place on a Welsh cap and the high regard in which the Welsh jersey is held within the squad.
"We will be looking to maintain and improve upon our performances against South Africa, Romania and New Zealand and play with the same high tempo, width and style which is fast becoming our trademark.
"We want to finish the series on a high and give the fans more of what they have enjoyed already. The RBS Six Nations is just around the corner and we need to go into our preparations for the kick-off match against England with a good performance against Japan under our belts.
"Each player selected is playing for their jersey's and for a place in the starting line-up against England.
"Jonathan Thomas will be our line-out captain and Gethin needs to be seen from the start on the tight-head side as we analyse all our options.
"In the backs, even though we have lost three players the pace and potential of the back line still looks top draw and the newcomers have got all to play for in terms of selection."
Wales: R Williams (Blues); H Luscombe (Dragons), G Henson (Ospreys), T Shanklin (Blues), S Williams (Ospreys); C Sweeney (Dragons), G Cooper (Dragons); Duncan Jones (Ospreys), M Davies (Neath RFC), G Jenkins (Blues), B Cockbain (Ospreys), J Thomas (Ospreys), Dafydd Jones (Scarlets), C Charvis (capt), M Owen (Dragons).
Replacements: S Jones (Dragons), A Jones (Ospreys), R Jones (Ospreys), A Popham (Leeds), M Williams (Blues), M Phillips (Scarlets), K Morgan (Dragons).
Japan: R Miki (World Fighting Bull); K Kubota (NEC Green Rockets), M Mukoyama (NEC Green Rockets), Y Motoki (Kobelco Steelers), H Daimon (Kobelco Steelers); H Yoshida (Kubota Spears), W Ikeda (Sanyo Wild Knights); Masahito Yamamoto (Toyota Motor Verbitz), T Yamaoka (Suntory Sungoliath), R Yamamura (Yamaha Motors), H Kiso (Yamaha Motors), T Kumagae (NEC Green Rockets), F Mau (World Fighting Bull), N Okubo (Japan RFU), T Miuchi (capt, NEC Green Rockets).
Replacements: Mitsuga Yamamoto (Sanyo Wild Knights), Y Hisadomi (NEC Green Rockets), T Yamaguchi (Kubota Spears), H Ono (Toshiba Brave Lupus), K Tanaka (Suntory Sungoliath), S Shimomura (Sanyo Wild Knights), K Sawaki. (Suntory Sungoliath).
Referee: Tappe Henning (South Africa)