Nigel Adkins and his Saints were looking for a much-needed second victory of the campaign after Morgan Schneiderlin put them ahead in the 65th minute but Swans winger Nathan Dyer came off the bench to grab an equaliser with just over 15 minutes remaining.
Southampton took a deserved lead 20 minutes into the second half when the French midfielder controlled Rickie Lambert's deft header before advancing into the area and around Swans keeper Gerhard Tremmel to make it 1-0.
However, the Saints were denied an elusive set of three points when St Mary's academy graduate Dyer pounced on Maya Yoshida's error to hammer home off the post and he was sure not to celebrate against his former club.
It was a harsh result for Adkins whose 19th-placed side had the better of the chances but unfortunately could not put them away as Michael Laudrup's Swans grabbed their 13th point of the campaign courtesy of a third draw from their past five.
St Mary's Stadium, Southampton - 30,501