The match was goalless in the 38th minute when Rotherham referee Webb pointed for what looked like a Southampton free-kick and, as both sets of players moved up field for the free-kick, Mr. Webb informed them a penalty had been given.
Many of the 32,054 crowd was stunned into disbelief, some thinking the decision had been given for handball and it was only later that it became clear the referee had decided Claus Lundekvam had pushed Juan Pablo Angel.
It was some minutes before Angel was able to take the penalty, sending Southampton goalkeeper the wrong way Antti Niemi for his 23rd of the season.
The appeals and arguments continued once play had resumed and Southampton coach Dennis Rofe was sent to the stands by Webb for continuing his protests too long and too loudly.
But the setback appeared to stir Southampton and in first-half injury-time Kevin Phillips ran onto a pass from Anders Svensson before shooting home from close range.
Even that goal had an element of controversy with Villa believing Phillips may have strayed into an offside position.
In a match of many incidents, a contrast to the normal end of season fare, both sides could have snatched a winner.
For Southampton Phillips, James Beattie and Svensson all went desperately close.
For Villa Angel might have done better with two second-half headers while Gavin McCann twice failed to make contact having stolen into dangerous positions.
But the star of the afternoon was undoubtedly the Saints goalkeeper Niemi who showed why so many rate him the best in the Premiership and why Arsenal are rumoured to be considering a bid.
Niemi made a superb interception in the 28th minute to block a header from Liam Ridgewell and then produced a truly world-class save to turn away a goalbound effort from Gareth Barry.
There was another save in the second half, sprawling on his line to deny substitute Peter Crouch as both sides made every effort to snatch a winner.
In contrast to Niemi, Villa keeper Thomas Sorensen had far less to do, plucking a free-kick from Phillips in injury time from the air to make sure Villa did not go home empty-handed.
Young Villa defender Ridgewell, up against the physical presence and power of Beattie, gave a polished performance alongside Ronny Johnsen.
Ridgewell, a former England Youth captain, might even have become a hero when his free header in the first half from a Barry corner allowed Niemi to show just why he has been so outstanding this season.
Svensson was the only player booked, for a clumsy late foul while Mr. Webb, for all his controversy, kept the match flowing and his cards in his pocket.
Man of the Match: Antti Niemi - Some brilliant saves confirmed his reputation as one of the Premiership's best goalkeepers.