Gatland told reporters Jones had failed a Head Injury Assessment, which would see him miss the trip to Edinburgh.
But subsequent tests which are more detailed have cleared the experienced lock and at this stage he has no signs of concussion, team officials confirmed on Tuesday.
Team doctors have been in contact with World Rugby to keep them abreast of the situation.
There may be more good news for Wales as prop Tomas Francis has responded well to treatment for a calf problem and looks set to be available.
Gatland insisted there were positives to take from the heavy loss to the Irish, in which Wales conceded nine penalties and three tries in the opening 20 minutes, a disastrous start from which they never recovered.
In particular he praised young centre Joe Hawkins (20) who earned his second cap and was one of the most impressive performers from either side.
"That’s what you want, a bit of backing from the head coach," Hawkins told reporters on Tuesday. "It's about not trying to be a different player, just go out there, and be confident in your own thing.
"It’s surreal being out on the training field with likes of AWJ (Jones) and Tips (Justin Tipuric). I'm trying to take in all their experience and then it's about putting it into your own game."
Hawkins was a livewire with ball in hand and along with his fellow rookie, wing Rio Dyer (23), provided plenty of danger for the Irish.
"I thought I had a decent game but there are bits to improve on. Since I was young, I’ve tried to be as rounded as possible. You can’t be one dimensional. I like ball playing but you have to bash it up sometimes.
"If selected (against Scotland) I’ll be really excited. There’s always a good atmosphere (at Murrayfield). It would be class to experience that."
Gatland will name his team for the test on Thursday.
