Nathaniel Clyne, fresh from making his England debut in the recent international break, scored his third goal of the season nine minutes from time to secure a share of the spoils.
Villa spent much of the first half under the cosh, but went ahead against the run of play thanks to the persistence of Gabby Agbonlahor, who capitalised on Fraser Forster's error.
Jores Okore made his first Villa appearance since September 2013 after a serious knee injury as part of three changes to Villa's back four, which was quickly put under siege by the visitors.
Southampton came into the game as one of the league's form side after five straight wins and went close three times in the opening 10 minutes as they looked to impose themselves on the contest.
Sadio Mane drew a flying save out of Brad Guzan as Southampton were unable to even the scores before the interval and Ronald Koeman began the second half with Dusan Tadic closer to Graziano Pelle in an attempt to penetrate Villa's stubborn defence.
Indeed, Villa should have doubled their advantage in the 78th minute. Andreas Weimann led a swift counter-attack that resulted in Agbonlahor squaring for the Austrian 12 yards out, but he launched his shot into the Holte End.
And he was made to pay just three minutes later, England defender Clyne providing perhaps an unlikely source of inspiration as his scorching effort gave Guzan no chance.
The point only moves Villa up to 16th, but draws against two of the league's in-form sides will boost confidence, while Southampton's failure to win leaves Chelsea a dominant six points clear at the top.
