The 26-year-old defender struck six minutes into the second half at Priestfield, adding to striker Rene Howe’s opener to see the Gills maintain their two-point safety margin ahead of next weekend’s finale.
Gillingham displayed attacking intent from the outset and Howe broke the deadlock after 18 minutes, slotting into an open goal from 10 yards after Saints’ goalkeeper Kelvin Davis’ clearance cannoned off Simeon Jackson.
Gowling doubled the lead shortly after the break, heading home Curtis Weston’s cross moments after Jon Otsemobor’s brave block had denied Jackson.
Southampton bounced back through David Connolly’s 20-yard strike in the 66th minute.
But while top scorer Rickie Lambert came close, the Saints couldn’t fashion an equaliser and Gillingham hung on for three valuable points.