After Marouane Fellaini had headed the hosts into a 1-0 half-time lead, Pienaar took control of the game by scoring a sensational second goal and then setting up Kevin Mirallas for the third.
Hal Robson-Kanu netted a deserved consolation for Reading six minutes from time, but they were second best throughout and have now lost their last three Premier League matches.
Everton made a flying start to the game and could have led within the first 60 seconds, when Leon Osman planted a left-wing cross on the head of Nikica Jelavic, only for the Croatian to nod his effort horribly wide.
Reading almost stunned the home crowd 28 minutes in after Everton failed to clear a corner and allowed Adam Le Fondre to thunder a right-footed shot against the top of the post.
Pienaar was in the thick of the action throughout the opening period and took his turn to go close when Leighton Baines reached the byline and cut back for the South African to release a goal-bound shot that Adrian Mariappa did well to block.
Jelavic then had another fantastic opportunity on the half-hour mark after being played through on goal by a hopeful punt from the back that Reading failed to defend, but his first touch took him slightly wide and his shot was saved by the legs of Stuart Taylor.
The breakthrough finally came four minutes from half-time. Seamus Coleman beat Ian Harte too easily on the right wing and delivered a superb cross for Fellaini to rise high and steer a header into the corner.
Reading started the second period brightly, but fell 2-0 behind on the hour courtesy of a wonderful goal from Pienaar, who cut inside from the right wing, stepped inside of Harte and then fired a left-footed rocket into the top corner from 20 yards.
Everton were suddenly rampant and Mirallas almost made it 3-0 three minutes later with a low, left-foot shot from an angle that shaved the far post.
He wasn't to be denied a goal, though, and duly got on the scoresheet in the 66th minute after latching on to a wonderful through-ball from the excellent Pienaar. Mirallas shaped to curl it into the far corner, but instead hooked the ball past Taylor at the near post.
Reading continued to battle for every ball and fully warranted scoring when substitute Robson-Kanu headed in Harte's pinpoint cross.