In his first game against his former team since leaving for European football seven years ago, Ruiz's Fulham were initially frustrated in a goalless first half.
But the returning hero made his mark in the second half by setting up the opening goal for Steve Sidwell to head home his corner in the 62nd minute.
Allen Guevara drew the home side level ten minutes later after finding space in the box to fire past summer recruit Maarten Stekelenburg, but Fulham quickly restored their lead.
A penalty was awarded for a foul on Alexander Kacaniklic after he was brought down by Elias Palma, and Dimitar Berbatov stepped up to coolly tuck away the spot-kick.
Ruiz then produced a fitting finish to the game when the Cottagers launched a swift break in the 87th minute and he struck at the near post.