Rickie Lambert opened the scoring in the 10th minute but Kenwyne Jones made amends for an awful miss by equalising with a smart backheel six minutes later.
A mistake from Robert Huth, who miscued a clearance against the bar, presented Jay Rodriguez with Saints' second in the 24th minute, and 12 minutes later Andy Wilkinson's own-goal made it 3-1.
Southampton should have extended their lead but Asmir Begovic saved Rodriguez's shot and Guly Do Prado missed an open goal from the follow-up, and they were made to pay as Stoke went down the other end and Matthew Upson scored from a corner in the 67th minute.
Steven Nzonzi was sent off four minutes later but Stoke kept pressing and got their reward in the 90th minute when substitute Cameron Jerome let fly with a stunning 30-yard volley that flew in off the underside of the bar.
Adkins said: "It's a fantastic point away from home. They had only conceded four goals at home this season and we've gone and scored three and could have scored more.
"We changed a few of the players round because we knew we had to deal with the aerial bombardment that would probably come during the course of the game. The players have been top drawer. At the end of the day it's a wonder strike from the lad."