Palace had to wait until the 73rd minute before James Scowcroft fired them in front with his eighth goal of the season.
But six minutes from time, Stern John earned the Saints a deserved point for their fifth consecutive away draw.
Despite a good playing surface for this time of the year, the football from both sides was somewhat scrappy particularly in the first 45 minutes.
However, both sides still had opportunities to break the deadlock.
The game was only ten minutes old when Adam Hammill delivered a wicked cross from the right which was glanced just wide by Jason Euell, who had only Julian Speroni to beat in the Palace goal.
The Eagles looked lively on the break and Ben Watson struck a firm shot from the edge of the box forcing Kelvin Davis to make his first save.
Andrew Surman and Hammill were playing well for the visitors in the centre of the park, while for Palace Ben Watson and Tom Soares were not being fed with decisive passes.
On 35 minutes Hammill fired wide as Speroni was slow to get across his goal and Andrew Davies chipped his shot wide of the upright.
Palace's best chance came on 41 minutes as Sean Scannell's low cross into the box found Watson 14 yards out and he looked set to score until Davies made a crucial block to save the day for Southampton.
Then right on half-time, Bradley Wright-Phillips missed a great chance as he failed to keep the ball down and Speroni watched gratefully as the ball flew over.
Southampton began the second half in a positive manner enjoying useful possession and often leaving Palace to defend deep.
Palace withstood the pressure and were now applying pressure themselves as Watson's shot took a deflection and flew past the post, while Clinton Morrison was unable to get enough bend on his 12-yard shot and once again the ball went just past the post.
The Eagles continued to plug away but their direct approach was easily contained by Southampton.
But on 73 minutes the Saints made a rare lapse in defence as a long ball from Clint Hill was allowed to bounce into the penalty area and Scowcroft turned from 12 yards out to tuck away a low shot into the bottom corner of the net.
Inspired by Scowcroft's goal, Palace went on to hit the woodwork twice.
Hudson headed against the post while Watson struck a screaming shot from 18 yards out that rattled the crossbar and over.
But Southampton soon recovered and on 84 minutes as on-loan defender John Halls was caught out of position and Marek Saganowski had time and space to deliver a low cross into the goalmouth for John to simply run the ball into the open goal to give the visitors a deserved point.