In a match of few chances Southampton created the best ones but had to rely on a blistering left-foot drive from 20 yards by Matty Oakley to give them the lead.
Oakley should have put Southampton ahead after 23 minutes but failed to make the best of a pass by Kamil Kosowski while Ricardo Fuller shot across the face of the goal as Southampton wasted clear openings.
Hull had Chris Brown booked for dissent in the 34th minute before Southampton got the lead they just about deserved.
A corner on the right Djamel Belmadi was only half cleared and Oakley struck a fierce shot with his weaker left foot past the unsighted Boaz Myhill.
In first-half injury time it needed a spectacular save by Antti Niemi to keep out a goal-bound header from Ryan France.
The second half was much like the first with Hull soaking up the pressure and Southampton unable to trouble Myhill except in the 53rd minute.
It was then that Nigel Quashie struck a fierce right-foot shot which Myhill turned around the post at full stretch.
Claus Lundekvam was unable to touch in a header from Brett Ormerod as Southampton kept pressing before Hull broke away to level.
Ellison, a 63rd minute substitute for Brown, broke free down the left and his shot from 15 yards at an angle surprised Niemi and went in off a post.
There were cries from disgruntled Southampton fans, calling for the chairman Rupert Lowe to quit and there was still time for a rousing finale.
Ormerod should have won the game for Southampton deep in injury time but he blazed over the bar from 15 yards after cutting in from the left and with the goal at his mercy.