Florent Malouda powered in the winner in the 83rd minute after latching onto Jose Bosingwa’s cross at Stamford Bridge.
Shane Long had taken just four minutes to put West Brom in front after dispossessing Alex and sidefooting past Hilario.
But Chelsea equalized in the 53rd when Nicolas Anelka cut inside and unleashed a shot that deflected off Jonas Olsson’ heel before landing in the far corner of the net.
Villas-Boas’ reign as Chelsea manager had started with a 0-0 draw at Stoke last weekend.
West Brom have now lost both of their opening matches.