The Welsh midfielder got up to take the spot kick and sent Mark Schwarzer the wrong way to score with a composed spot kick.
Fulham looked for a quick response through Berbatov, but his shot on the turn was scuffed wide from range.
Berbatov was involved again soon after with an instinctive flick towards goal, with Alex McCarthy well placed to save with relative ease.
At the other end Danny Guthrie sent a swerving strike from distance just wide of the target as Reading continued to pose a potent attacking threat.
Reading held firm to lead at the interval, with Riise firing well wide late in the first half.