Warburton moves to openside flanker and regains the captain's armband after Gethin Jenkins led the side in last weekend's 24-20 victory over Argentina.
Liam Williams starts at fullback with Halfpenny moving to the wing and there is an all-new front-row for Wales with Nicky Smith, Scott Baldwin and Samson Lee, who all started on the bench against Argentina, called into the starting side.
“We have made a number of changes but have named a very experienced side,” said Rob Howley, who is Wales head coach while Warren Gatland is on secondment to the British and Irish Lions.
“We have made a change with Liam (Williams) moving to fullback and Leigh (Halfpenny) onto the wing. Leigh has done well at fullback but we are giving an opportunity to Liam, it’s his favourable position, Leigh has played on the wing before.
“Japan are a much changed side from the Rugby World Cup but Jamie (Joseph) is developing his team and their recent performances echo the dangers of the RWC with their ability to move the ball wide early and they are a great counter-attacking team."
Lloyd Williams plays at scrumhalf with Gareth Davies on the bench while Alun Wyn Jones will win his 104th Wales cap and starts in the second row with Cory Hill, who will make his second test appearance.
Wales: 15-Liam Williams, 14-Leigh Halfpenny, 13- Jonathan Davies, 12-Jamie Roberts, 11-Alex Cuthbert, 10-Gareth Anscombe, 9-Lloyd Williams; 8-James King, 7-Sam Warburton (captain), 6-Dan Lydiate, 5-Alun Wyn Jones, 4-Cory Hill, 3-Samson Lee, 2-Scott Baldwin, 1-Nicky Smith
Replacements: 16-Kristian Dacey, 17-Rhys Gill, 18-Scott Andrews, 19-Jake Ball, 20-Ross Moriarty, 21-Gareth Davies, 22-Sam Davies, 23-Keelan Giles
(Reporting by Toby Davis; editing by Ed Osmond)
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