Baker, 23, and Thornton, 20, trained with Wales ahead of the 2015 World Cup, but were omitted from the squad.
Both have signed three-year deals, taking the total of players on NDCs to 16, with Ospreys contributing half.
Their salaries funded 60% by the Welsh Rugby Union and 40% by the regions.
Baker has been capped three times and Thornton led Wales Under-20 in the 2015 Six Nations.
The duo's deals were announced a day after Ospreys hooker Scott Baldwin and back-five player James King signed dual contracts.
Baldwin, 27, was his country's first-choice hooker at the recent World Cup and has signed until 2019.
Lock or back-rower King, 25, has secured a deal until 2018.
The deals, which give the Welsh Rugby Union more control over players, were introduced to help stem the exodus of stars such as Toulon's Leigh Halfpenny from Wales.
Newport Gwent Dragons number eight Taulupe Faletau turned down a dual contract in May 2015 and Bath's recent bid to sign him was vetoed by Wales coach Warren Gatland.
Baker, Thornton, Baldwin and King have signed against a backdrop in which fly-half Rhys Priestland has taken an 18-month Test rugby sabbatical to concentrate on playing for Bath after leaving Scarlets.
Gatland said: "Dan and Rory are players of significant potential.
"We look forward to continuing to work with them at national squad headquarters, but also to watching them continue to flourish for the Ospreys."
Fly-half Biggar is expected to sign a contract extension, but lock Jones is considering his future beyond the end of the 2015-16 season.
Wales captain Sam Warburton was the first of the nation's current generation to commit to a dual deal.

The Portuguese, 39, replaced Mike Phelan in January on a deal until the end of the season but could not save them from the drop to the Championship.
He led Hull to six wins from his 18 Premier League games, with relegation confirmed after a 4-0 defeat by Crystal Palace on 14 May.
In a statement, Hull said they were "disappointed" by the departure of a "firm fans' favourite".
The club were relegated in the penultimate week of the season and Silva said at the time: "It's my goal as a manager to work in the Premier League."
The former Sporting Lisbon and Olympiakos manager has been linked with Watford after the dismissal of Walter Mazzarri, but said recently he had not received an offer from the Hornets or any other club.
"Everyone knows when you have the chance to work in the Premier League, you don't want to work in Championship, it's normal," he said last week.
A statement from Hull said Silva "will be forever remembered for his efforts to maintain our Premier League status".
It added: "Unfortunately, after considering his future, he has chosen to leave in order to further his career."
Assistant head coach Joao Pedro Sousa, first team coach Goncalo Pedro and goalkeeping coach Hugo Oliveira have also left the club.
BBC Radio Humberside sports editor Matt Dean:
Marco Silva is undoubtedly a loss, although his departure isn't exactly a surprise. His drive, energy and focus for the job was unwavering and his values rubbed off on his players and the fans. He was always viewed as a coach bound for bigger things and brighter times.
The club will be hard pressed to find another in his mould. Whoever gets the job will have to pick up the pieces of a squad shorn of six loan players now back with their parent clubs and be capable of galvanising those left, including the fans. There are no guarantees either that players such as Harry Maguire, Andy Robertson and Abel Hernandez will remain at the club.
Fans will watch with keen interest to see how serious the club's owners are to get the club back to the Premier League with the next appointment and the resources allocated to them.
Ospreys number eight Dan Baker and uncapped lock Rory Thornton have become the latest Welsh players to sign national dual contracts (NDC).
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Marco Silva has resigned as Hull City manager after the club's relegation.