With seconds remaining Bent picked up a pass from fellow substitute Duncan Ferguson, forced his way into the box and rifled an unstoppable shot into the top corner past keeper Paul Smith.
Southampton looked to be heading to only their second league win under new boss Harry Redknapp when they came from a goal down to nearly snatch all three points.
The home side did not get off to the best of starts when former striker James Beattie, once loved on the south coast, scored after just four minutes.
Beattie, who hit 76 in 233 matches for the Saints grabbed his second goal for his new club following a long throw by James McFadden.
The Scottish winger's long hurl into the box found Tim Cahill. whose header was saved by Smith only for Beattie to smash home the rebound from a tight angle.
The home side almost got back on terms after 13 minutes following a mistake from Everton captain Alan Stubbs. His tame pass fell to Peter Crouch who fed on loan striker Henri Camara, only for the Senegal striker to blast his shot wide of the post from eight yards.
Beattie continued to haunt his old side and almost grabbed a second with a chance after 19 minutes. Joseph Yobo's long ball forward found the striker on the edge of the area and he fired a first-time volley which Smith did well to push round the post.
Smith was again called into action after 26 minutes when Claus Lundekvam played a short back pass. The pacey James McFadden just managed to beat the keeper to the ball but the legs of Smith saved Southampton as the ball ran to safety.
The home side began to get into their stride midway through the first half and after heavy pressure equalised in the 36th minute.
Rory Delap's long throw on the right found Crouch six yards out and he made no mistake with a looping header into the top corner.
Three minutes before the break Crouch almost put his side in front, only for his drilled effort to be cleared off the line by Alan Stubbs.
In the second half the Saints took control with Camara causing problems for Everton. After 52 minutes Camara got in the box to force a god save from Nigel Martyn before going one better three minutes later.
He played a one-two with David Prutton before hitting a low right foot shot past Martyn to give his Saints a deserved lead.
Everton boss David Moyes put on striker Ferguson to cause problems for the Saints defence. He also gave a debut to Mikel Arteta, who replaced a tired Alan Stubbs after 59 minutes.
With the Toffees searching for an equaliser Southampton broke away and another Camara effort was saved by Martyn.
But when it looked like the points were in the bag for the home side, Ferguson and Bent combined to snatch what could be a vital point for their Champions League quest.