The 25-year-old started at outside-centre for the 33-20 win over Italy at BT Murrayfield, and held onto his place in the XV against the Irish, but sustained knee ligament damage against Joe Schmidt’s side, who ran out 22-13 winners.
Scottish Rugby said in a statement that it was “unlikely” the Glasgow Warriors midfielder would feature again in the 2019 championship.
“The Glasgow Warriors midfielder sustained knee ligament damage in the national team’s round two defeat to Ireland at BT Murrayfield Stadium on Saturday, with scan results suggesting the injury recovery time would likely be beyond the reaches of the current campaign,” the statement added.
Jones, who has 50 points from 17 appearances for Gregor Townsend’s side, has returned to Scotstoun for treatment from the Glasgow medical staff but there was still uncertainty over Warriors colleague Stuart Hogg.
The full-back damaged his shoulder in the early stages of the match against Ireland, and was replaced by Blair Kinghorn.
It was reported earlier this week that the 26-year-old, who will join Gallagher Premiership side Exeter Chiefs in the summer, could miss the remainder of the PRO14 season depending on the nature of his injury.
However, the 66-times capped Scotland international has not yet been ruled out of the remaining three matches against France, Wales and England.
A statement from Scottish Rugby said: “Stuart Hogg damaged shoulder ligaments early in the first-half of the [Ireland game] and is now under the joint care of the Glasgow Warriors and Scotland medical teams, with his rehabilitation progress and review ongoing.”
Scotland haven’t had their injury problems to seek. A total of 19 players, including John Barclay, David Denton, Richie Gray and Duncan Taylor, were ruled out through injury ahead of the Six Nations, while Glasgow’s Ryan Wilson has since been ruled out for the remaining three matches after sustaining a knee injury. The Aldershot-born forward’s withdrawal leaves Scotland light in the back-row, with John Hardie, Blade Thomson, Sam Skinner and Hamish Watson all sidelined along with Barclay and Denton.
However, Magnus Bradbury will feature for Edinburgh in their Guinness PRO14 match with Dragons this weekend and has already been tipped as a solution to the back-row selection crisis by head coach Richard Cockerill.
Glasgow’s Fraser Brown has since been added to the national squad following his return from injury, while Murray McCallum was also called up for the Ireland game.
Brown’s Scotstoun team-mate Zander Fagerson is also understood to be closing in on a return to action but it remains uncertain if he will be fit enough to play any part in the remainder of the Six Nations.