Russell Slade's side fell behind to Byron Moore's 53rd-minute opener, but two goals from substitute Chris Dagnall, in the 60th and 67th minutes, turned the result around and sent Orient back to the summit at the expense of Brentford, who were held 1-1 at Walsall.
Clayton Donaldson put Brentford in front on the half-hour mark, but Craig Westcarr's leveller on the stroke of half-time earned a share of the spoils and brought to an end the visitors' run of eight consecutive league victories.
Preston North End's Kevin Davies enjoyed a day of mixed fortunes at Deepdale in his side's 1-1 draw with Coventry City.
The damage was done inside the opening 21 minutes as Tom Hitchcock, Ben Pringle and James Tavernier all found the net for Steve Evans' side, who claimed their second successive win.
At the bottom, Callum Ball's 42nd-minute goal handed Notts County a 1-0 win at Stevenage, who remain at the foot of the table, while Bristol City drew 2-2 at home with MK Dons.
Sheffield United and Bradford City also drew two apiece, while Gillingham and Port Vale finished 2-0 and 1-0 home victors over Swindon Town and Oldham Athletic respectively.
Colchester United triumphed 4-2 at struggling Carlisle United, while third-placed Wolves' fixture at Crawley Town was postponed due to a waterlogged pitch.
