Spurs had looked set to clinch all three points at St Mary's after maiden strikes by Pedro Porro and Ivan Perisic were sandwiched by Harry Kane's 23rd goal of the campaign.
Ruben Selles' bottom-of-the-table side had scored only twice in their previous five league appearances but showed the same fight that saw them recently take points off Chelsea and Manchester United to come back from 3-1 down to boost their survival hopes.
Ward-Prowse's late penalty, after Pape Sarr had fouled Ainsley Maitland-Niles in the area, added to second-half efforts by Che Adams and Theo Walcott to earn Saints a share of the spoils.
Tottenham were unchanged from their win over Nottingham Forest, which meant another opportunity for Richarlison but he left the pitch after five minutes with an injury to see his hapless season take another turn for the worst.
Saints were required to make a substitution of their own soon after with Armel Bella-Kotchap forced off with an injury to his right arm and the hosts should already have been ahead by this point.
Adams fired wide from close range in the third minute from Ward-Prowse's scuffed effort after Stuart Armstrong saw a low strike blocked by Clement Lenglet.
Following a stop-start opening at St Mary's, the contest settled down with Southampton dominate in possession but the visitors continued to create the better opportunities and Porro sliced two good openings over.
It was not long before the injury curse returned with Jan Bednarek encountering an issue around his rib area on the half-hour mark.
Bednarek initially continued before he was forced off and Ben Davies became the fourth enforced substitute of the first half when he suffered an injury to his right leg in the 38th minute.
While Saints' new centre-back pairing of Mohammed Salisu and Maitland-Niles were getting accustomed to each other, Spurs pounced to break the deadlock in first-half stoppage-time.
Son Heung-min spotted Porro in space on the right and passed the ball into the path of the January recruit, who took a touch and thundered an effort in off the crossbar to open his account for Tottenham.
It took 43 seconds for Adams to level for Southampton after half-time and become the first Southampton forward to score in the Premier League this year.
Romeo Lavia split Lenglet and Perisic with a perfectly-weighted ball into Walcott, who squared for Adams to slide in for his 10th goal of the season in all competitions.
Ward-Prowse clipped the roof of the visitors' net with a free-kick minutes later before Kane signalled his intentions by sending a curled effort over after carrying the ball from inside his own half.
Southampton did not heed that warning and with 65 minutes played, Kane scored for the seventh time at St Mary's.
Substitute Dejan Kulusevski floated a ball to the back post where Kane powered home a header for his 23rd goal of the season.
When Perisic opened his account for Spurs in his 36th appearance with a half-volley beyond Gavin Bazunu in the 74th minute, the points appeared wrapped up for the visitors.
Yet Selles' side had other ideas and Walcott reduced the deficit from Sekou Mara's knock down three minutes later to set up a dramatic finale.
Former Southampton goalkeeper Fraser Forster thwarted Mara from close-range soon after but the hosts would not be denied.
Tottenham substitute Sarr caught Maitland-Niles in the area following a corner and Ward-Prowse, who saw his last spot-kick against Leicester saved, made no mistake this time and fired into the corner to earn Southampton a precious point.