The Blues won 1-0 at AFC Wimbledon, Michael Smith netting the decisive first-half goal to secure their League Two play-off spot.
However, Jones didn’t reappear after the break having picked up a problem in the first-half.
He was replaced by Brian Murphy for his first Pompey appearance since Ipswich Town at home in the FA Cup in January.
The former QPR stopper proceeded to put on a solid display to help Paul Cook’s side to their Kingsmeadow triumph.
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Cook was already without nine players through injury at the Wombles.
Now he’s awaiting news on the extent of Jones’ setback after the keeper had recently re-established himself in Pompey’s team.
The Blues boss said: ‘Jones had a problem with his thigh, it’s where we are at the moment.
‘He said he kicked it and felt something pop, we’ll have a look at it. That’s footy.
‘Brian Murphy is an excellent keeper, his shot-stopping and distribution is second-to-none.’
Matt Clarke (groin) and Marc McNulty (hamstring) were missing from the side which defeated Wycombe at the weekend.
They joined absentees Adam Webster (ankle), Ryan Fulton (thigh), Kyle Bennett (ankle), Conor Wilkinson (groin), Conor Chaplin (groin), Jack Whatmough (back) and Ben Tollitt.
Meanwhile, Cook opted to move Ben Davies to the bench, putting Kieron Freeman in at right-back for only his second Pompey start.
To fill the substitutes, Pompey called-up Academy pair Adam May and Christian Oxlade-Chamberlain, along with Brandon Haunstrup.