Wales will look to bounce back from their opening day defeat to England as they face Scotland in a must-win Six Nations clash at Murrayfield tomorrow.
Gatland claimed Jones was not fit enough to be considered for a starting role.
But a lack of dynamism in the back-line has been a major criticism of Wales in recent times, and it appears Jones would have been demoted regardless of injury.
Ryan Jones replaces the injured Andy Powell at number 8 - the only other change to the side which lost 26-19 to the old enemy.
The selection of Hook in the pivotal stand-off position has provoked much discussion, with speculation suggesting Jones should have been retained, and others calling for youngster Rhys Priestland to start.
Hook has yet to start a game at number 10 for his club side The Ospreys this season, but has impressed in cameo appearances.
And he was switched from full-back when Jones was substituted last Friday evening, albeit with mixed success.
Gatland hopes the man regarded as the most talented ball-player in the Welsh back line can flourish in his first international start at fly-half since 2009.
The Ospreys man will attack the line and should prove a threat with ball in hand, but the highly-rated Scottish back row - and openside flanker John Barclay in particular - will label him an immediate target.
For Hook to be effective, Wales require a much improved performance from scrum-half Mike Phillips, who was disappointing against England.
Injury to last week’s substitute Dwayne Peel means Phillips starts but his place is coming under increasing scrutiny.
And the Wales head coach will also be hoping for an improved performance from outside centre Jamie Roberts who was anonymous against England.
Gatland said: “Against England Jamie didn’t get his hands on the ball until 41 minutes into the game. But there is a responsibility on Jamie to go looking for the ball.”
Ryan Jones’s selection to replace Powell is less surprising, although he has not been in form and was stripped of the Welsh captaincy following the Fiji debacle last November.
The Welsh management have retained the same pack for what promises to be a colossal showdown with a Scottish pack looking to bounce back from a French domination in Paris.
But Scotland’s struggles in the French game come more from Gallic brilliance than their own failings and their were encouraging signs in defeat, not least in the three tries they scored.
With only seven tries in Andy Robinson’s first 13 games in charge, Scotland threw off the shackles with Alistair Kellock, Kelly Brown and Sean Lamont all touching down.
And a return to Murrayfield is sure to further inspire a Scottish side who inflicted the only defeat on world champions South Africa during the autumn internationals.
The Scottish pack is stronger on paper than Wales, with Euan Murray, Richie Gray, Nathan Hines and Barclay all strong ball-carriers. In contrast, Bradley Davies, Sam Warburton and the injured Powell were the only Welsh players to make significant yardage last Friday.
As ever, Wales possess the greater individual brilliance in the back-line, with Phillips, Roberts, Shane Williams and Lee Byrne all Test Match Lions.
But they need to click as a unit to drag Wales out of their dismal run.
A return of just two wins in 13 games leaves Gatland under intense pressure and defeat tomorrow is unthinkable.