The Belgium striker met a left-wing corner with a downward header that bounced high into the net in the 80th minute, earning his team only its third victory in 14 matches.
The goal settled a scrappy game between two teams that are set to be involved in a relegation battle this season. Reading stayed second from bottom but is now just four points clear of Queens Park Rangers, which drew 0-0 at Sunderland.
Benteke had a weak shot saved and Brett Holman blazed over with Villa's other good chances.
Reading is without an away win in seven matches since returning to England's top flight.
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