Lockwood's penalty early in the second half wiped out Crewe's first-half advantage given to them by the ever-dangerous Nicky Maynard.
It was Orient's tenth point from a possible 12 which has lifted them from the foot of the table to 18th place this month.
Orient survived an early scare when Maynard charged down a clearance from Justin Miller and raced clear but home goalkeeper Glyn Garner made a smart stop.
But gradually the O's started to take control as Gary Alexander chested the ball down for strike partner James Walker who fired just wide.
Miller atoned for his earlier error when he went on a wriggling run from deep but saw his effort charged down before Luke Guttridge had an effort blocked.
But gradually Crewe's five-man midfield took a vice-like grip of the game and Orient were indebted to keeper Garner who saved well to deny Michael O'Connor.
Orient boss Martin Ling was forced into an early change when Miller departed the action suffering from illness and was replaced by Shane Tudor.
The O's still threatened on the break as Walker had a shot well saved by Stuart Tomlinson before Alexander raced into the area and fired a chance inches wide.
But it was Crewe that struck first when they caught Orient on the break.
Ben Rix played in an astute ball to striker Maynard who swivelled in the area and fired across Garner into the far corner of the net.
The goal knocked the stuffing out of the home side who then had to replace Tudor with Donny Barnard as the substitute picked up an injury just before the break.
But the O's could not have wished for a better start to the second half when within 60 seconds Billy Jones was adjudged to have fouled Walker and Lockwood blasted home the spot kick to Tomlinson's right.
After that Orient looked the more likely winners as skipper John Mackie headed over then Guttridge fired wide.
But it was Crewe who could have stolen a winner on the break when Luke Varney missed a glorious chance when he found himself 12 yards from goal with only Garner to beat but the O's keeper saved well.