The Saints eventually ran out convincing winners on the South Coast, but that was only after Fulham had found themselves 2-0 within 25 minutes of the start.
Lee Clark, starting his first game for 17 months, and Steed Malbranque had struck to set The Cottagers on their way, but Gordon Starchan's men showed tremendous resolve to comeback and they dragged themselves level before the break.
A penalty and then a brilliant header from Beattie gave him a first half brace and meant the score was 2-2 at the interval, after which Southampton took control.
Beattie helped himself to his third, whilst strike-partner Brett Ormerod grabbed a deserved goal when registering Saints' fourth.
Fulham were well beaten, but will have wondered how they allowed Southampton back into the game, after being two goals to the good.
Their first came after just 14 minutes and was the first meaningful effort of the whole game.
Clark took a quick free kick with Rufus Brevett before attempting to play the ball into his strikers, Anders Svensson intercepted the ball, but the former Newcastle man followed the ball in and won a fifty-fifty challenge with the Swede.
He then found himself 30-yards out from goal and unleashed an effort which took a wicked deflection off Michael Svensson, which sneaked into the corner and left Antti Niemi stranded at the other side of the goal.
The strike was Clark's first goal for six years, since he found the net for Newcastle - ironically against Southampton.
The impressive Fabrice Fernandes then tested Edwin van der Sar with a free kick on the edge of the area, but it was held by the Dutchman.
The Saints also had a very good penalty appeal turned down after 19 minutes when Steve Finnan appeared to nudge the ball with his upper arm, but the home fans appeals were in vein, as referee Mark Halsey waved play-on.
Then Fulham countered with a wonderful break and made it 2-0. Irish full back Finnan played the ball into Luis Boa Morte, who in turn played in Steve Marlet.
The French international then found Finnan in the area - who had carried on his run - and he pulled the ball back for Malbranque who evaded a statuesque Saints defence and blasted the ball into the top corner from 15 yards.
The Cottagers looked to be in control, but just a minute later Southampton were back in the game when they were awarded a penalty after central defender Alain Goma deflected the ball out of Ormerod's path with his left arm. Beattie stepped up to convert his second penalty in six days and beat van der Sar with ease.
Beattie then missed a great chance to equalise just minutes later. Chris Marsden took a quick free kick from the left and he found the burly striker, but he could not get the contact he wanted and it deflected off his shoulder and over.
The ex-Blackburn man, though, then found the net with a brilliant header just before half time.
A good piece of play down the right by Southampton saw Fernandes pick up the ball near the sideline before cutting in and delivering a vicious cross which found Beattie, who had lost his marker Zat Knight, and headed firmly back across van der Sar and into the corner of the net.
Just after the break Southampton almost grabbed the lead through an uncharacteristic mistake from skipper van der Sar.
The Dutch ace had the ball in hand and opted to throw, but instead of finding one of his players, he threw straight to Fernandes. The Frenchman took the ball on into the area and delayed before unleashing a shot which deflected of Brevett and just evaded Beattie, who came within an inch of grabbing his third.
But Beattie was not to be denied his first senior triple strike when he sealed his hat-trick with another very good header after 53 minutes.
The Saints won a free kick on the Fulham right, which Anders Svensson swung into the area, Beattie rose unmarked and headed down powerfully into the bottom corner leaving van der Sar with little chance.
Fernandes was the chief tormenter against his former club all day and in the second half looked particularly dangerous and he once again created the chance from which Southampton converted their fourth.
The midfield ace broke deep into Fulham territory before spotting the run of Marsden - his movement was tracked by Brevett who covered well, but his attempted tackle fell into Oremerod's path and he made no mistake from ten yards as he cooly slotted underneath van der Sar to make it 4-2.
The Saints did have other chances to extend their lead, the best coming when Michael Svensson almost converted a free kick from namesake Anders.
Southampton boss Gordon Strachan also took the opportunity to give Ecuadorian Agustin Delgado his first taste of football for almost a year when he replaced Ormerod with just over ten minutes remaining - he had one chance which van der Sar saved but looked lively in his brief showing.
Fulham were poor in the second half, but still came very close on more than one occasion in a late spurt towards the end of the game.
Sylvain Legwinski's overhead kick from Boa Morte's cross was just wide and then Niemi pulled off a wonderful save to prevent substitute Barry Hayles getting on the scoresheet when he turned brilliantly in the box.
Fulham's final effort came when Marlet burst into the area and unleashed a shot which he pulled just past Niemi's far post, although that would have been more than the Londoners deserved.
Southampton were well worth their victory and Fulham's two goals were almost flattering to Jean Tigana's side - who now see The Saints move above them into ninth.
After a bright start to the season, Fulham are beginning to fade although still ninth, whilst Southmapton's very good home form looks to be giving them a firm bed to push for a place in the top half of the table.
