The 29-year-old missed a penalty – his dinked effort was saved by Kelvin Davis – but scored twice late on to earn United a 3-2 win at St Mary’s.
“His first goal was magnificent – the control and then to bury it. It was a really good goal,” said Ferguson.
Robin van Persie has reached 100 Premier League goals in 197 games, the eighth-quickest rate in the competition’s history
“His header was excellent, too, but he has been a terrific player for us.”
The Netherlands international, who moved to Old Trafford from Arsenal for £24m during the summer, equalised for the visitors after Rickie Lambert put Southampton ahead, but United fell behind again when Morgan Schneiderlin headed in shortly after half-time.
Van Persie was then the villain when his chipped spot-kick was saved, before scoring twice in the final three minutes to give his new side an unlikely three points.
“I was surprised [at Van Persie's spot-lick] because every time I have seen him take a penalty he rattles it in the corners,” said Ferguson.
“He made up for it, though. He had six attempts on goal and was a real threat. But we didn’t start playing until Paul Scholes came on the pitch, to be honest. I thought he changed the game right around.
“We worked all week on the strength of Southampton with their back-post crosses and they scored two goals from it.
“We have got to give them credit for that, they are good at it. In that period when they scored the second we were well out of it.
“Paul Scholes came on and brought composure, a consistency of passing and made the difference.”
Van Persie scored his first goal for the club against Fulham last week and now has four in two starts since leaving Arsenal.
“It was a good feeling afterwards,” said the striker. “But I’m very disappointed with the penalty. When that happens at 2-1 down, you can’t take a penalty like that. Something went wrong big time.
“I have to say a big thank you to Paul Scholes. Every single pass he hit was the right one. It was unbelievable. He is man of the match for me.”