Lisbie struck from the penalty spot after Orient's Luke Ashworth handled Kem Izzet's goal-bound effort on the line and was sent off.
It ended a League One game of few real chances and a particularly lacklustre first half.
Kayode Odejayi dragged a shot wide of the far post with only goalkeeper James Jones to beat while Orient threatened sporadically, with Sean Thornton nodding over from close range and then drilling a shot into the side netting.
The closest the hosts came to scoring before the break when Jones tipped away Anthony Wordsworth's downward header from Marc Tierney's curling cross.
Home keeper Ben Williams tipped over Ryan Jarvis' fierce effort on the hour mark and then foiled Eric Lichaj soon after, as the O's pressed.
Thornton cleared Phil Ifil's diving header off the line from Wordsworth's corner and Williams foiled Jarvis, before Lisbie held his nerve from 12 yards.