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The Seagulls, who pipped the Berkshire side to the second division title last season, frustrated the Royals again with a vital win.
But they owed much to Reading keeper Marcus Hahnemann who gave them two helping hands with a blunder in each half.
The American keeper opened the door for Brighton in the 17th minute when he inexplicably handled a back-pass from full-back Graeme Murty. Whilst many fans considered the referee's decision harsh, Marcus was clearly to blame.
With striker Bobby Zamora bearing down, Hahnemann panicked and picked the ball up, and Brighton were quick to take advantage as Zamora's swift free-kick allowed Paul Brooker to stroke the ball into an empty net.
The goal stunned fourth-placed Reading into action and they should have been level before half time, only to be frustrated by a well-drilled Brighton defence.
Steve Coppell's side were tactically outstanding and Reading grew increasingly frustrated as first Nicky Forster shot over with the goal at his mercy and then debutant Glen Little twice went close.
The winger, on loan from Burnley, saw a header brilliantly nodded off the line by Kerry Mayo midway through the first half and Little was denied again when his stinging volley was stopped by veteran Brighton keeper Dave Beasant, who recovered his ground well after going AWOL from his goal.
Reading were denied a blatant penalty in first-half stoppage time when Forster tumbled under Mayo's challenge but they continued to press in the second half. TV replays showed that there was no doubt the Royals should have been awarded a spot kick.
Forster was agonisingly close to an equaliser when he outstripped Ivar Ingimarsson and drilled a shot across the face of goal, but Reading's fightback was ended by a killer Brighton goal in the 77th minute.
Richard Carpenter's deep free-kick was headed on by substitute Paul Kitson just four minutes after the much-travelled striker had come on.
The effort looked easy pickings for Hahnemann yet the usually reliable shotstopper somehow managed to fumble the ball across his own goal-line.
Reading pulled a goal back four minutes from the end courtesy of a brilliant volley from substitute Jamie Cureton, whose curling effort dipped past the helpless Beasant.
But the damage had already been done and Brighton held on for what could prove to be a vital victory.