The striker joins Saints from Queens Park Rangers, for whom he scored 18 goals in the Barclays Premier League last season – a campaign that ended with his first call-up to the senior England squad.
26-year-old Austin, who has netted 130 times since moving into professional football with Swindon Town in 2009, will join up with his new teammates next week.
Les Reed, Southampton’s Executive Director of Football, said: “We are very happy to be able to welcome Charlie to the club.
“Coming after Wednesday’s morale-boosting home victory, this signing is an indicator of our intent to finish the season strongly and continue the progress we’ve made in the last few years.
“Charlie shares that ambition. He has a fantastic goalscoring pedigree, but remains hungry to improve and develop as a footballer – something that convinced him that Southampton is the ideal next step in his career.
“Having had a taste of Premier League football and his first call-up to the England squad last season, he is determined to establish himself at the highest level of the game.
“Bringing Charlie here is a show of the club’s commitment to its plan for future success through investment in talent with a desire to grow and develop.”
Austin added: “I'm delighted to have got it over the line so soon into January. I can't wait to get started now.
"As soon as Southampton showed an interest that was the one club I wanted to go to.
"You see the progression from when I was playing against Southampton for Swindon. For me, it was important to come to a club that's on the up and that's what I've got here."