Matthew Lockwood put Orient ahead from the penalty spot after Stephane Gillet fouled Paul Connor.
Orient sealed victory in the second-half when Connor volleyed home Gary Alexander's cross.
Chester had opportunities but Ben Davies struck the post and Paul Tait failed to convert the subsequent rebound, missing from five yards.
Chester boss Keith Curle left the Deva Stadium shortly after Saturday's defeat amid rumours that he has parted company with the League Two strugglers. Curle and Chester chairman Stephen Doyle left the ground without comment after the club's 11th defeat in 12 league games.
The poor run has left them just four points above the drop zone.
Chester: Gillet, McNiven, Artell, Dimech, Regan (Richardson 78), Walker (Blundell 70), Drummond, Curtis, Davies, Tait (Asamoah 84), Branch.
Subs Not Used: Stephen Vaughan, Hessey.
Booked: Gillet, Davies, Dimech.
Leyton Orient: Garner, Miller, Zakuani, Mackie, Lockwood, Easton, Simpson, McMahon (Demetriou 90), Keith (Barnard 68), Alexander, Connor (Steele 88).
Subs Not Used: Tann, Morris.
Booked: Keith, Easton, Connor, Barnard.
Goals: Lockwood 35 pen, Connor 72.
Att: 2,210
Ref: T Parkes (W Midlands).
MMIX
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