The hosts were completely in charge for most of the game and grabbed a vital victory over a Magpies side looking bereft of ideas to earn three points and move up to 17th place
Adam Lallana's simple tap-in and Gaston Ramirez's second-half strike proved the difference as the hosts dominated for large periods.
The win moves Southampton within three points of the Magpies, and lifts them out of the relegation zone at the expense of Aston Villa.
Frazer Richardson and Richard Chaplow were the only absentees from the Saints squad as Nigel Adkins named the same side that beat QPR last weekend.
Alan Pardew made five changes after Hatem Ben Arfa was added to Newcastle's ever-growing injury list against Maritimo on Thursday night. Yohan Cabaye was also out while Fabricio Coloccini served the last of a three-game ban. Papiss Cisse made it into the side despite coming off in their Europa League draw.
The home side started brightly, putting pressure on the visitors as they searched for their second win, but it was Newcastle who fashioned the first real chance of the game with a Demba Ba header.
Ramirez then had a shot blocked after a fine solo run as the hosts had the better of the opening 10 minutes. The Uruguay international nearly broke into the area shortly afterwards but was stopped on the edge of the box, much to the annoyance of Adkins.
The pace of the game petered out as the first half passed the half-hour mark. Southampton were looking bright going forward but were wary of being caught out on the break.
But the hosts got a deserved goal on 35 minutes after Rickie Lambert hit the bar with a free kick. Tim Krul's poor clearance allowed Nathaniel Clyne to fire the ball back in to Ramirez, who slid the ball across to Lallana to finish and send the home fans into delirium.
Pardew threw on Sammy Ameobi at half-time in the hope of fashioning more of a threat down the left flank, and the visitors had the first chance of the half as Cisse headed at Paulo Gazzaniga.
Vurnon Anita was then put through on goal but pressure from Fonte was enough to but the midfielder off and he drove straight at the goalkeeper. The hosts immediately burst up the other end and Lallana had a close-range shot parried by Krul, who stood firm.
The Newcastle goalkeeper then gifted the hosts a second moments later as he parried Puncheon's cross straight into the feet of Ramirez, who blasted high into the net to double the lead.
Puncheon nearly made it three soon after when he latched on to the end of Lallana's pass and drilled the ball into Krul's near post.
It was then Gazzaniga's turn to be tested as the Saints shot-stopper produced a stunning save to keep out Davide Santon's header, which looked like sneaking in low at the near post.
The woodwork was called into action again as Fonte's looping header hit the bar and Lallana was denied by Krul once more before substitute Jay Rodriguez had a goal ruled out for offside, but the home side had done enough to earn a vital three points.