The home side had taken a 15th minute lead through Matt Lockwood, but Southend came storming back and netted twice in a deadly seven-minute spell through Freddy Eastwood and Wayne Gray.
It had all started so brightly for injury hit Orient looking for the win that might have pushed them into the top three.
The game was just 15 minutes old when Orient's new loan signing Daniel Chillingworth headed the ball through for Scott, who was bundled over in the area by defender Lewis Hunt.
Lockwood stepped up and fired home from the spot, but before Orient could build on their lead the Seasiders hit back with a vengeance.
Skipper Kevin Maher was the architect of both goals. First his free-kick was floated into the Orient area and Eastwood and saw his effort roll over the line.
Then Maher sent in a corner from the right that was won by Hunt and as the ball bobbled around Gray, who had spent a loan spell at Orient, scrambled the ball home from close range.
Orient skipper Alan White should have levelled on the stroke of half-time, but blazed over from close range before the livewire Chillingworth went close in the second half.
And it was the Orient debutant who set up the leveller just before the hour with the perfect right-wing cross for Scott to send his shot crashing past Bart Griemink in the Southend goal.
Chillingworth almost marked his debut with a goal as Orient went looking for the winner, but Southend were always a threat on the break and ex-O's man Adam Barrett saw a close-range effort skim off the bar.
But it was Orient who finished strongly as Wayne Carlisle and Scott both had late chances to win the game.