The Cottagers started the day as Championship leaders but they were trailing from the 19th minute when Ejaria found the top corner with a curling shot from the edge of the box.
And the former Liverpool youngster, 23, produced an even better effort in the 53rd minute as he collected Alen Halilovic's chipped pass on the turn and side-footed past Cottagers keeper Paulo Gazzaniga.
But Reading held on in the face of strong late pressure to record back-to-back successes for the first time this term while Fulham slumped to a second defeat in three games.
Marco Silva's side had responded to their first loss of the campaign at Blackpool with a comfortable 4-1 victory at Birmingham midweek.
And they looked as though they would quickly build on that success when they immediately pressed Reading backwards with Bobby Decordova-Reid and Mitrovic both going close.
Reading had ended a winless four-game run with victory over Peterborough this week and they began to threaten once they had settled into the match.
And they forced the lead when Ejaria finished following a sweeping move.
Halilovic drove forward on the right before squaring for John Swift who moved the ball quickly on to Ejaria and the left-sided midfielder cut in onto his right foot before beating Gazzaniga.
The switch did little to affect Reading and Swift came close to adding a second when he sent a well-struck free-kick just wide of Gazzaniga's right-hand post.
Fulham struggled to recover the momentum they had built up in the opening stages but Decordova-Reid spurned a good headed chance and Mitrovic was left frustrated when he struck the bar in first half added time.
But it was Reading who struck the next blow when Ejaria doubled the lead with a superb finish.
Halilovic was again at the heart of the move, intercepting Tim Ream's pass to launch the counter-attack and was then on hand to chip a superb return pass into the path of Ejaria who turned as he controlled the ball before slotting home.
Muniz's first Fulham goal gave the home side hope but they were unable to find an equaliser.