North End went into the clash at Brisbane Road just two points off top spot in League One, unbeaten away from home this season and having won their last seven matches. And the status quo looked like being maintained after just two minutes as Jamie Proctor raced down the left flank and crossed for the unmarked Paul Coutts to score from close range.
Orient took some time to recover their composure but levelled after 36 minutes when Kevin Lisbie jinked his way past a defender and picked out Cox, whose header rolled past Andreas Arestidou before nestling into the corner of the net.
The goal galvanised the O’s and the hosts went in front in first-half injury time when Cox surprised Arestidou with a perfectly-placed drive from 25 yards.
The second half was just three minutes old when Scott Cuthbert conceded a penalty for a push on Neil Mellor but Lee Butcher dived to save Graham Alexander’s spot-kick.
The visitors were out of luck when Iain Hume thumped a free-kick against an upright, and the home side defended doggedly to earn all three points for the first time this term.