Prutton jumped into a tackle on Robert Pires to leave referee Alan Wiley no option but to dismiss him.
But that was not the end of the matter as the angered Prutton pushed referee Wiley in the chest and had to be restrained by club physio Jim Joyce as well as Redknapp.
In the time added on for the stoppage Arsenal scored a goal through Freddie Ljungberg to deflate Southampton who had fought so hard through the first half.
A goal behind and down to ten men, relegation-worried Southampton faced the prospect of a heavy beating but the game was far from over.
Arsenal were also reduced to ten men when striker Robin Van Persie was dismissed in the 52nd minute.
Like Prutton, Van Persie had been fortunate to stay on when he received only a yellow card after appearing to elbow Southampton defender Rory Delap.
But there was no escaping his fate a second time when a lunge at Graeme Le Saux left the former England full-back on the ground injured.
Redknapp added: "Luckily Arsenal had a stupid player on their side as well.
"Van Persie got what he deserved without a doubt and you can tell Arsenal were upset with him by what Arsene Wenger said to him as he left the field.
"The Arsenal sending-off squared it up and gave us a chance.
"At half-time we were a bit despondent because we had worked so hard to stay in the game and yet we were down to ten men and a goal behind, so we had to have a go and keep attacking Arsenal.
Arsenal made four changes from the side beaten in Bayern Munich in midweek and they were never at their best although they enjoyed the majority of possession.
In an even first half it was the Arsenal goalkeeper Jens Lehmann who was the busier, swooping to keep out a low shot from the pacy Henri Camara.
But deep into stoppage time, after Prutton had been led away, Arsenal took the lead when Henry held off three tackles to leave Ljungberg with an open goal.
The second half belonged to the rookie Saints goalkeeper Paul Smith who made a succession of outstanding saves to deny Arsenal a second goal.
But the dismissal of Van Persie gave Southampton heart and they were level in the 67th minute.
Jamie Redknapp took a corner on the left and with Lehmann a long way from his line, Peter Crouch was able to head in an empty net for his ninth of the season.
Crouch almost got another one two minutes later when he raced clear on to a Redknapp path, but shot across the face of the goal.
In the end though had to thank Smith for enabling them to preserve a much-needed point.
In the 49th minute he somehow deflected a shot from Henry wide from six yards at the start of a hectic spell of Arsenal pressure.
In the 79th minute the former Brentford keeper was at full stretch again to turn a header from Pascal Cygan over the bar.
Arsenal's star man Ashley Cole raced clear in the 85th minute but again Smith made a superb block to keep out the shot.
Crouch went close at the other end with a header from a centre by substitute Paul Telfer but the main action was at the other end.
Deep into injury time Smith made another vital interception to keep out an Henry shot, but there was drama to the very last.
In the final seconds Cole had the ball in the Southampton net, but celebrations were cut short by a referee's flag indicating an offside decision.
Arsenal manager Arsene Wenger, said: "We have played worse than this and won so I am not complaining"
"In the last 15 minutes we had three or four good chances but their goalkeeper kept them in the game.
"Of course I am disappointed not to have won. When you are 1-0 up and the opposition is down to ten men the immediate target is to keep all 11 of your players on the pitch.
"So losing Van Persie so early in the second half was a setback.
"At half-time Van Persie had time to calm down but he was at fault with the tackle.
"I thought we looked solid in the air and in the end we got caught on one corner. Otherwise we played very well."
Man of the Match: Paul Smith - Four outstanding saves in the second half earned Southampton a vital point and denied Arsenal a morale-boosting win.