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.
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.
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.
Jay Emmanuel-Thomas fired Bristol in front in the 36th minute, but James Dayton's late equaliser forced both sides to share the spoils.
And Rotherham and Colchester United played out a 2-2 draw, while Preston North End's fixture against Tranmere Rovers ended at 1-1.
