Boyd has impressed since joining the Wellington Phoenix while Thomas has made a strong start at Dutch Eredivisie club PEC Zwolle. Since signing in the middle of 2013, the 19-year-old has earned a contract extension through to 2018, scoring his first league goal for club two weeks ago in a 2-1 victory over Roda JC.
Five players are included who didn't feature in the playoff loss to Mexico with Payne, Howieson, Thomas and Boyd joined by Wellington Phoenix defender Michael Boxall, who is aiming for his first All Whites appearance since 2012.
"The players deserve to be in the squad,'' Emblen said. "They are getting regular game time and playing a high level of football. They are in good form and deserve the opportunity.''
"It's going to be a huge test. Japan play fantastic football and I expect they'll be at full strength because their players will be aiming for selection for the World Cup.''
Despite stepping out as a head coach at senior international level for the first time, Emblen will not be on unfamiliar ground, having visited the National Olympic Stadium before as a player for the Club World Cup and as a coach in the lead-up to the London Olympics. It will be the final game for the home side at the venue before the World Cup.
"I've had good experiences there and I'm familiar with the stadium and I like Tokyo so I'm not going into the unknown,'' said Emblen, who will be assisted by Junior All Whites coach Darren Bazeley.
"It's going to be an historic occasion and I'm honoured to be doing it. It's a privilege and I'm thankful I've been given the opportunity and I'll be doing my best to help the side be as ready as they can be to put in a good performance.''
The March 5 fixture against Japan, who are heading to this year's World Cup, honours an agreement to reschedule an international friendly the All Whites withdrew from due to safety concerns after the earthquake that struck the country in March 2011.
All Whites squad to play Japan in Tokyo on March 5: Glen Moss (c), Jacob Spoonley, Ben Sigmund, Bill Tuiloma, Storm Roux, Michael Boxall, Andrew Durante, Michael McGlinchey, Chris James, Ryan Thomas, Tim Payne, Cameron Howieson, Tyler Boyd, Shane Smeltz, Marco Rojas, Jeremy Brockie, Kosta Barbarouses, Chris Wood.