Neither side produced much in the way of chances in a tepid first half although Northampton's Louis Moult saw his goalbound shot charged down and Jake Robinson's fierce drive was superbly tipped over by Jamie Jones.
Moult should have put Northampton ahead just before the break when he raced onto Ishmel Demontagnac's defence-splitting pass but shot straight at the advancing Jones.
Clive Platt also had a close-range shot blocked by Scott Cuthbert just after the restart but it was Orient who broke the deadlock in the 56th minute. Moses Odubajo's cross was knocked down by Ryan Brunt and Mooney scored at the second attempt after his initial effort was blocked on the line.
Moult fired over as Cobblers looked for an equaliser and Emyr Huws was denied by the outstretched leg of Jones after he jinked his way into the box.
But Orient doubled their lead in the 65th minute when Mooney converted another Odubajo cross at the far post.
Orient wrapped the game up in the 73rd minute when substitute Michael Symes scored from the penalty spot after Joe Widdowson handled in the area.