Freddie Sears fired Mick McCarthy’s side into the lead just before close of a lacklustre first half, during which both teams struggled to carve out many clear-cut chances.
Former Ipswich forward Daryl Murphy levelled the scores on his return to Portman Road, slotting home an equaliser just after the hour mark.
But David McGoldrick restored Ipswich’s lead just seven minutes later, tapping home from close range before Emyr Huws’ volley sealed it in stoppage time.
The hosts had the ball in the net just before the quarter hour mark, as Tom Lawrence’s inswinging free kick from the left crept past the outstretched arm of Karl Darlow and into the bottom right-hand corner. Referee Tim Robinson, however, had already blown his whistle for a foul on Jamaal Lascelles in the box.
United’s first sight of goal came shortly after, when Christian Atsu whipped a cross onto the head of former Ipswich frontman Murphy, whose header took a deflection on its way over. The resulting corner was cleared as far as Paul Dummett, whose venomous drive flew past the upright.
After Jonjo Shelvey’s well-struck volley had been gathered by Bartosz Bialkowski, a dummy from Dummett at the other end gave the Welsh international the chance to cross. Though Matt Ritchie stooped to connect, his header bounced into the ground and over Bartosz Bialkowski’s crossbar.
Less than five minutes later, though, the deadlock was broken. United surrendered possession in the middle, allowing Lawrence to run at the backline. He spotted Sears in space on the left, slid it into his path and, despite the best efforts of the retreating Ritchie, the former West Ham man’s sidefooted finish found the target.
And just a couple of minutes later, McGoldrick could have made it two from an almost identical position, but his drive was deflected over.
The Tractor Boys carried that momentum into the second half, while Newcastle continued to find it difficult to find any gaps in the resolute home defence. Lawrence curled another free kick over the top, and Benitez responded with an attacking substitution, replacing Isaac Hayden with Yoan Gouffran on the hour.
And just seconds later, the visitors finally found a way through. Atsu delivered an inviting low cross from the left and, though Gouffran narrowly failed to connect at the near post, Murphy – who earlier received a warm reception from the Ipswich faithful – was well placed in the middle to turn the ball home and level the scores.
However, just seven minutes later, Town went back in front. When United didn’t fully clear their lines, the hosts poured forward, and Sears broke into the box before squaring for McGoldrick to tap home from close range.
Benitez’s side rallied, with Atsu looking particularly lively down the left flank and Aleksandar Mitrovic introduced in place of winger Ritchie, but despite fleeting sights of goal for both the Serbian forward and centre back Grant Hanley – whose header was held by Bialkowski – the hosts sealed it in time added on, when midfielder Huws met a cross from the right with an emphatic volley, giving Darlow no chance.