The striker scored his 17th goal of the season with a brilliant half-volley after just 70 seconds to settle the game.
The Saints dominated possession but rarely threatened the Albion goal as the Baggies kept their seventh clean sheet in 10 games under head coach Tony Pulis.
The closest Southampton came to an equaliser was when Chris Brunt deflected Ryan Bertrand’s second-half cross just wide.
West Brom are now eight points clear of the Barclays Premier League relegation zone in 13th, having lost just once under Pulis.
Southampton, though, are clinging onto fifth place having won just once in their last five games.
The Baggies were unchanged while the Saints brought back Bertrand, Morgan Schneiderlin, Dusan Tadic, Florin Gardos and Sadio Mane, after the forward had been dropped after being late in the build-up to their 2-0 defeat to Liverpool.
Berahino had shaken off a minor knock to start and he made an instant impact after just 70 seconds.
Brunt’s lofted free-kick was headed out by Maya Yoshida but only as far as Berahino and the striker unleashed a rasping half-volley which flew into the top corner from 16 yards.
The striker is prolific at The Hawthorns, with 15 of his 17 goals this season coming at home.
The Saints were ragged and Fraser Forster saved Claudio Yacob’s header before Gardos was replaced by Elijero Elia.
Boss Ronald Koeman had seen enough and his side almost responded when Mane fired over after collecting Schneiderlin’s brilliant cross-field pass.
The change altered the game’s dynamic and the Saints improved, although they failed to test Ben Foster as Mane shot off target again.
Craig Gardner almost found an opening when he failed to control a long ball when clean through but it was a rare chance for the Baggies.
Their defensive organisation, which has now seen them keep four straight clean sheets under Pulis, was evident though.
Despite having the bulk of possession and pinning Albion back, Southampton struggled to break down the massed Baggies ranks.
Steven Davis replaced Victor Wanyama at the break and referee Phil Dowd also failed to reappear, with fourth official Graham Scott taking charge.
And Albion suffered a blow 10 minutes into the second half when Berahino limped off to be replaced by Youssouf Mulumbu.
It took away the Baggies’ best outlet and Southampton continued to press and almost levelled after 67 minutes.
Bertrand linked well with Elia on the left and when Graziano Pelle missed his cross, it deflected inches wide off Brunt.
Brown Ideye wanted a penalty after tangling with Fonte during a rare Albion raid with 10 minutes remaining.
And the visitors could have levelled with four minutes left when Pelle latched onto a Schneiderlin header only to mis-hit his shot straight at Foster.