A quality strike from Yeovil substitute Arron Davies helped his side stay in second place and ruin Orient's comeback.
Yeovil, two goals to the good at half-time, looked liked cruising to their fifth away win of the season.
But injury-hits Orient came storming back in the second half with strikes from Efe Echanomi and Dan Chillingworth before Davies settled the match with his excellent goal.
Chances were far and between early on, but Yeovil took the lead after 25 minutes when Lee Johnson threaded the ball threw to Bartosz Tarachulski, who calmly chipped the ball into the net from 14 yards .
Orient tried to hit back but suffered another blow on the stroke of half-time.
Yeovil's Paul Terry fired in a free-kick from the right which eluded everybody including Orient's keeper Glen Morris and somehow drifted into the net, much to the delight of the Yeovil player .
The goal gave Orient a mountain to climb, especially without their three frontline strikers Gary Alexander, Lee Steele and Jabo Ibehre - all on the treatment table .
However, the home side hit back hard in the second half. Orient's manager Martin Ling threw 17-year-old Echanomi into the action and he responded with a goal.
Midway through the half Chillingworth headed on Justin Miller's long throw and the young striker reacted first to fire home his first senior goal from six yards.
Then seven minutes later it looked like Orient's comeback was complete when Chillingworth grabbed his first goal for the club.
He rifled the ball home from 20 yards after Echanomi cut the ball back from the left .
However, Orient's comeback was short-lived as Yeovil regained the lead three minutes later when Davies smashed the ball into the corner of the net from 25 yards.
Orient strove to respond and skipper Micheal Simpson headed inches wide in the last minute .