The O's looked dead and buried as they trailed 3-0 with just 13 minutes remaining and they looked like crashing to their fourth straight defeat.
The visitors were in cruise control as goals by Mark Bentley and Guylain Ndumbu-Nsungu just before the break put them in the driving seat.
And when the livewire Matthew Jarvis struck in the second half, Gillingham looked racing certainties to wrap up the points, but then Lockwood took centre stage and smacked home a penalty on 77 minutes followed up with two more goals to leave the Gills shell-shocked.
The game had started at a frenetic pace as O's manager, Martin Ling, opted to play with three strikers and the move almost paid dividends.
The game was just two minutes old when striker Gary Alexander sent a header floating inches wide.
Little was seen of the Gillingham attack during the early stages, although O's keeper Glyn Garner was forced into a smart stop when he blocked a shot by Andrew Crofts and Jarvis fired the rebound wide.
But the complexion of the game changed on 43 minutes when Danny Jackman crossed from the left following a short corner and Bentley came rushing in to head home.
Orient's misery was compounded in stoppage time when Jarvis went on a great left-wing run and cut the ball back for Ndumbu-Nsungu to fire into the net from six yard.
The rampant Gills then grabbed a third on 57 minutes when the ever dangerous Jarvis twisted and turned defender Brian Saah, before firing in a shot that took a deflection off of the defender and nestled in the corner of the net.
But then came the revival. On 77 minutes Adam Chambers was felled by Scott Flinders and Lockwood stepped up to fire home the penalty past the keeper's left hand.
Minutes later Lockwood picked up a short corner from Daryl McMahon and drilled the ball into the net and the comeback was complete a minute from time.
Lockwood latched on to McMahon's through ball and fired home an unlikely leveller from a tight angle.