Portsmouth's three-goal blitz in the first 11 minutes helped to bring an end to Newcastle's unbeaten home record.
Benjani scored Portsmouth's second with a sweet volley
Noe Pamarot's vicious strike put Pompey ahead before John Utaka muscled past Claudio Capaca to slot in and Benjani did the same before volleying home.
Newcastle hit back on 15 minutes when the ball went in off Sol Campbell after Michael Owen's shot had been saved.
But Pompey added a fourth on 71 minutes when Niko Kranjcar's free-kick went in via Steve Taylor's knee.
It was no more than Portsmouth deserved after they produced an assured and incisive display.
Newcastle can have no complaints after some diabolical defending particularly from Brazilian centre-back Capaca, who was hauled off after only 18 minutes to be replaced by David Rozehnal.
But there was little anyone could have done to prevent Pompey's opener after only eight minutes.
A corner was cleared to Pamarot and he returned the ball from 25 yards with ferocious pace and accuracy, straight into the top right corner.
But after the sublime came the ridiculous when, a minute later, Cacapa hesitated and was easily shoulder-barged out of the way by Benjani, who then curled in a sweet left-foot volley.
And two minutes later, Utaka repeated the trick, muscling past the shell-shocked Cacapa before rounding keeper Steve Harper and slotting into an empty net.
However, Newcastle were handed a lifeline shortly after when a series of ricochets went their way.
David James was unfortunate after saving Charles N'Zogbia's shot and Owen's follow-up only for the ball to hit Campbell in the chest and bounce into the goal.
Incredibly, Newcastle almost got themselves right back in the game as Taylor forced a good save out of James at his near post.
Yet they still looked vulnerable at the back and Rozehnal almost carried on where Capaca had left off when he appeared to handle in the area but he escaped conceding a penalty.
Newcastle did settle down a little after that, but it always seemed Pompey could raise their game should they wish.
After the break the visitors seemed content to sit back, stay disciplined in defence and make sure of their first win at St James' Park since 1949.
The hosts attempted to force the game, with Owen and James Milner bringing saves out of James.
But they never really looked capable of clawing their way back into the match.
And another defensive lapse ended any glimmer of hope they might have had as Taylor could only deflect Kranjcar's free-kick past Harper.
It could have been even worse for Newcastle but Pompey substitute Kanu was denied a goal by the crossbar.
That they did not concede a fifth goal will be scant consolation for Sam Allardyce as he ponders his first home defeat since taking over as Newcastle boss.
Newcastle boss Sam Allardyce:
"Disappointed is an understatement - I am devastated by what has happened here today. I am completely gutted inside.
"The players have be organised, understand how they should play, keep their shape, keep their discipline.
"Portsmouth did not have to put us to the test because we gifted them the game in those 12 minutes."
Portsmouth assistant coach Tony Adams:
"It was an excellent performance, with some great individual displays. We kept the ball really well and that was really pleasing.
"We have made a conscious effort this year to get more points on the road.
"I think our formation, playing with an extra man in midfield, really helps us out. And I thought that we were excellent today."
Newcastle: Harper, Taylor, Faye, Cacapa (Rozehnal 18), Jose Enrique (Martins 57), N'Zogbia, Butt, Barton, Milner (Emre 69), Smith, Owen.
Subs Not Used: Forster, Geremi.
Booked: Smith, Butt.
Goals: Campbell 16 og.
Portsmouth: James, Pamarot, Distin, Campbell, Johnson, Davis, Muntari (Pedro Mendes 87), Diop, Utaka, Kranjcar, Mwaruwari (Kanu 76).
Subs Not Used: Ashdown, Lauren, Taylor.
Booked: Distin, Davis.
Goals: Pamarot 8, Mwaruwari 9, Utaka 11, Kranjcar 71.
Ref: Chris Foy (Merseyside).