First Sean Hessey saw red for stamping on O's skipper Gary Alexander at the start of the second half and then substitute Joe O'Neill was also sent off late in the game for elbowing Orient defender Gaby Zakauni.
It was a game that Orient dominated from start to finish, especially after Chester lost defender Phil Bolland early on with a head injury.
The home side grabbed the lead following a flowing move that saw Alexander's clever ball send Echanomi clear and he calmly beat former O's keeper Chris MacKenzie.
Michael Branch wasted a good chance to level six minutes later following a rare Chester raid, but it came as no surprise when Orient stretched their advantage just past the half-hour mark.
Chester failed to clear the danger after Lockwood whipped in a free-kick that was saved by MacKenzie and when Alexander set up Echanomi, he was flattened by Hessey.
Lockwood stepped up and slotted the penalty into the corner past MacKenzie's despairing left hand - it was the defender's sixth league goal of the season.
Orient continued to press and almost added a third when Daryl McMahon fired an effort against the foot of a post and then had another chance ruled out for offside.
After the break any hopes Chester may have had quickly disappeared when Hessey was dismissed.
Orient failed to press home their numerical advantage as they frittered away possession.
But they should have added to their tally as Derek Duncan hit the bar before Michael Simpson blasted a golden chance over.
Alexander also had a header ruled out for offside before Chester's day got even worst in the 89th minute when substitute O'Neill, who had only be on the pitch for six minutes, was dismissed following a challenge on Zakauni.