Teenage forward Nadir Ciftci looked to have given Pompey all three points o Saturday in his first league start for the club after scoring on his full debut in the Carling Cup at Stevenage on Monday.
But the Royals were not to be denied and Mali winger Kebe got on the end of a Gylfi Sigurdsson cross to spoil the party for cash-strapped Pompey.
Sigurdsson struck the post in the second half as the visitors rallied after going behind to Ciftci's early strike.
Pompey started brightly and were rewarded with a goal just seven minutes in.
Ciftci took a short corner from the right to Matt Ritchie, who returned the ball to the Dutchman and his right-foot strike appeared to take a deflection before beating Royals goalkeeper Adam Federici.
Ritchie tried his luck from 25 yards out five minutes later but the winger failed to test Federici.
But Pompey boss Steve Cotterill was dealt a blow after 17 minutes when John Utaka's participation finished prematurely due to injury and Joel Ward came on to replace him.
The Royals had their first goalscoring opportunity after 21 minutes when Jobi McAnuff found space but flashed a right-foot drive over the crossbar.
David Nugent had a chance to double Pompey's lead but the former Preston striker fluffed his volley from 12 yards out.
Highly-rated midfielder Sigurdsson tried his luck with a volley from just outside the Portsmouth area but the ball sailed over the bar.
Ritchie could have given the home side a two-goal lead at the break but his left-foot effort was off target.
Iceland midfielder Sigurdsson was unfortunate eight minutes into the second half when his free-kick from 30 yards out came back off the post with Jamie Ashdown beaten.
On-loan defender Ibrahima Sonko could have opened his account for Pompey against his former club but headed straight at Federici.
McAnuff was presented with an opportunity on the hour mark but the former Watford man failed to hit the target from close range.
Simon Church should have done better 20 minutes from time when he volleyed wide from six yards out and Royals boss Brian McDermott reacted by bringing the Welsh striker off, with long-term injury victim Noel Hunt coming on to make his first appearance since last October.
It looked as though Reading would be consigned to a second defeat in as many Championship games but with four minutes left Sigurdsson swung in a corner from the left and Kebe stabbed home from six yards out to silence the Fratton Park faithful.