Chester extended their unbeaten run to five games against bottom club Luton.
Kevin Ellison wasted two great early chances for Chester but it was Luton who went ahead just before half-time.
Claude Gnakpa kept the ball in play at the byline and Rossi Jarvis flicked on for Asa Hall to volley into the top corner from 15 yards.
Luton had chances to add to their lead before Paul McManus headed in a Ryan Lowe free-kick and Chester had Kevin Roberts sent off for a second booking.
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