A superb 30 yard shot from Orient substitute Chris Tate denied Albion Reserves victory.
Yesterday's Avon Insurance League game at Brisbane Road finished in a 3-3 draw.
The Seagulls had taken an eighth minute lead when David Lee won a tackle just outside the penalty area before slotting home.
The lead was shortlived as the O's equalised from the penalty spot eight minutes later when Shaun Wilkinson tripped John Martin. Will Packham saved the initial kick from Jones, but the Orient player slammed the rebound home.
Although Charlie Oatway was substituted on the half-hour with a slight hamstring strain, the visitors continued to dictate and they regained the lead nine minutes after the resumption when Daniel Webb met Lee Steele's cross to head home.
Kevin Hemsley seemed to have made the game safe for Brighton in the 68th minute when he applied the finishing touch to a free-kick from substitute Stefan Wojciechowski.
But Lysden Christie was left unmarked to head home a corner in the 72nd minute before Tate struck with a minute left.
Albion: Packham, Wilkinson, Jackson, Rogers, Hemsley, Mayo, Lee, Webb, Steele, Oatway (sub: Wojciechowski 31), Samson (sub: Beck 61). Unused subs: Bridle, Greatwick.
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