Gary Megson's side were frustrated for the majority of the contest in the Black Country, but Lee Hughes scored with 11 minutes left to earn The Baggies another win towards promotion back to The Premiership.
West Brom threatened early on as Thomas Gaardsoe missed with a header from Jason Koumas's free kick while Sean Gregan forced Gills goalkeeper Steve Banks into a save from 20 yards out.
Geoff Horsfield had a glorious opportunity to give West Brom the lead, but he missed from close-range from Koumas's free kick.
Eight minutes after the break Koumas forced Banks into another fine save, before The Gills saw Mamady Sidibe fire a shot from 25 yards out that West Brom keeper Russell Hoult stopped.
With 11 minutes left, substitute Lloyd Dyer proved decisive again for The Baggies as his cross found Hughes at the far post to convert and give West Brom a vital winner.
The Baggies are eight points clear of third place Sunderland while Gillingham's fifth successive defeat sees them a point above the relegation zone in Division One.
Nationwide Division One
West Bromwich Albion 1-0 Gillingham
