Peterborough could have gone level on points with Orient with victory, but are now six points behind Russell Slade's side after David Mooney struck twice for the winners.
The 29-year-old, who has now scored 11 league goals, got his first just before half-time to cancel out Tommy Rowe's effort.
Dean Cox put Leyton Orient in front four minutes after the resumption, before Mooney's second sealed the win.
Wolves kept the pressure on Orient with a 2-0 home win over Stevenage, keeping them three points behind the table-toppers.
Kenny Jackett's side are now unbeaten in seven league fixtures after Kevin Doyle and Karl Henry scored in their latest win.
Saturday's action also saw Coventry City and Swindon Town post big victories, with the former defeating strugglers Notts County 3-0.
Leon Clarke struck twice in the second half, while Calvin Wilson also netted after the break, as a 10-man County side dropped to the bottom of the table.
Swindon saw off the challenge of Port Vale with a 5-2 success, although they needed goals in the last 10 minutes from Nathan Byrne and Australian Massimo Luongo to seal their triumph.
Luongo had also scored earlier, as his effort - in addition to strikes from Dany N'Guessan and Nile Ranger - helped Swindon into a 3-0 lead.
Tom Pope and Lee Hughes quickly scored for the losers though, setting up an exciting finish at the County Ground.
Bristol City climbed off the foot of the table despite being denied a victory in a 1-1 home draw with Oldham Athletic.
Jay Emmanuel-Thomas fired Bristol in front in the 36th minute, but James Dayton's late equaliser forced both sides to share the spoils.
Fellow strugglers Crewe Alexandra also claimed a point, in a goalless draw against Bradford City, while Sheffield United lost 2-0 at Shrewsbury Town.
Other results saw Gillingham and MK Dons post 1-0 wins over Carlisle United and Walsall, while Brentford won their fourth match in a row after defeating Crawley Town by the same score.
And Rotherham and Colchester United played out a 2-2 draw, while Preston North End's fixture against Tranmere Rovers ended at 1-1.
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