Wednesday have now only won one of their last six games and occupy sixth place, just a point above Fulham who host Wolves on Saturday.
Reading’s Danny Williams saw his low shot deflected wide early on.
Wednesday’s first effort of the night came when Barry Bannan’s cross from the right was met by Jordan Rhodes, whose header was comfortably saved by Ali Al-Habsi.
Bannan then supplied a cross which picked out Sam Winnall, who headed wide.
Kermorgant put the visitors ahead in the 13th minute, cutting in from the right and slotting the ball beyond Keiren Westwood’s reach, into the far corner of the net.
As Wednesday looked for a swift response, Adam Reach shot wide and Winnall fired in a low effort which was easily dealt with by Al-Habsi.
Morgan Fox went close to equalising midway through the half when he controlled the ball just outside the area and saw his effort strike Al-Habsi’s left-hand post.
Reach fired over and was then involved in another chance for the hosts. He tried a shot from inside the area which deflected off Liam Moore, the ball looped into the air and was met by Rhodes who headed wide.
Soon after the re-start, Rhodes went close with a near-post flick from Bannan’s free-kick.
Rhodes directed a header on target from Bannan’s corner, but it was straight at Al-Habsi.
Reading midfielder John Swift created space for himself before firing just wide from the edge of the area.
Kermorgant found himself free on the right-hand side of the area and played the ball across the face of goal, but there was no-one there to apply the finish.
Wednesday head coach Carlos Carvalhal made a change in attack midway through the second period, sending on Steven Fletcher in place of Winnall.
And Fletcher was soon involved, firing in a shot which was deflected off-target.
It was the start of a good spell for the home side, firstly with Will Buckley forcing a double save from Al-Habsi.
Substitute Callum McManaman then had a shot parried and the ball fell to Buckley, whose ball across the face of goal just evaded Rhodes as the striker stretched to try and connect with it.
The impressive Al-Habsi was called into action again, producing a good save to keep Buckley’s effort out.
Deep into stoppage time, substitute Popa added a second, finding the unguarded net after goalkeeper Westwood was left stranded after going upfield.