As reported by Goal.com on Monday, the Frenchman had hoped to make his return to first team contention after a knee injury against Manchester City on Sunday.
Kaboul played 48 minutes before being replaced by Jack Barthram having sprinted for a ball and subsequently complained of an upper leg problem.
Tottenham told Goal.com that Kaboul's withdrawal was planned, but witnesses say that the defender limped off.
The former Portsmouth center back played an hour in another Under-21 match against West Ham last week after returning to full contact training in late March.
He had been sidelined since undergoing surgery in August and may now have to deal with another setback after a successful outing against the Hammers.
Spurs are currently missing William Gallas after the veteran suffered a calf strain in the first leg of their Europa League tie against Basel, but Michael Dawson, Jan Vertonghen and Steven Caulker are fit.