Jones was driven from the pitch at the Aviva Stadium in a medical cart in the 71st minute after falling awkwardly while attempting to catch a high ball.
An MRI scan undertaken revealed damage to one of the stabilising ligaments in his foot, requiring six weeks of immobilisation.
The development means Jones, who was making his full Test debut on Saturday, is no longer under consideration for Ireland's 30-man squad for the World Cup, which is named on Monday lunchtime.
The 24-year-old Munster full-back had played his way into contention for New Zealand, though his lack of experience counted against him.
"The squad and management are bitterly disappointed for Felix to suffer an injury at such a vital time in terms of selection for the final touring party," said manager Paul McNaughton. "He had certainly put himself into contention during pre-season and the games in the last three weeks.
"We all wish him a speedy recovery and that he is back playing as soon as possible."
Jones was an option to supply back up to first choice full-back Rob Kearney at the World Cup, but coach Declan Kidney may now be forced to rejig his plans.
Kidney is unlikely to turn to Geordan Murphy after he was picked to play against Connacht in midweek, so it appears as though Luke Fitzgerald or Keith Earls will be asked to fill the role.
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