Two early goals from Andrew Halliday and Merouanne Zemmama and a second half close range goal from Richard Smallwood put Boro in the hat for the fourth round, despite Jack King's goal before the interval and some high-tempo, enterprising football from the visitors.
The visitors' boss had made 11 changes to the side that defeated Championship table-toppers Blackburn in Lancashire on Friday night an in torrential conditions back in the Red Rose county, they triumphed despite a lot of pressure form the Lilywhites.
It was a first half of two halves, with the visitors coming out of the blocks similar to the way North End have become renowned this season, but then North End dominating the last 20 minutes of the period with some high pressing, free-flowing football.
But it was the Championship visitors who came of the traps the better in the Monsoon conditions, where the pitch belied the weather, looking and playing superbly, allowing both sides to play a slick passing game.
Tony Mowbray’s outfit won a series of early corners, Emmanuel Ledesma with some dangerous deliveries from the right and one of the those crosses led to the ball eventually finding Andrew halliday, who tried an audacious chip that Steve Simonesen tipped over.
However, it was from another corner that brought the Reds the lead. A Merouane Zemmama free kick was blocked by the North End wall and Ledesma swung over the corner right under the cross bar. It looked to have crossed the line directly from the cross, but Halliday made sure by sliding in and poking home from close range with 13 minutes on the clock.
And the lead was double five minutes later with a nice passing move by Boro. They spread the play wide to Halliday on the left who in turn fed the ball into the edge of the box. It was laid off to Zemmama who struck the ball low from 25 yards, beating Simonsen and ending up in the bottom left hand corner.
This goal, however, almost prompted North End into action. Manager Graham Westley matched up the visitors’ 4-2-3-1 formation and they began to press their opponents and gain plenty of the ball, zipping it about from side to side, getting Amoo and Monakana in the play.
A number of crosses came in with King twice heading just wide of the right hand post and North End, who were well behind after 20 minutes, started to dominate the corner count.
Just after the half hour mark a superb spell of passing saw Mousinho, playing at right back, combine well with Amoo that led to the former Liverpool man cross to Stuart Beavon at the front post. He turned and flicked the ball goalwards, but Leutwiler did brilliantly in the goal to block for a corner.
However, North End were back in the game five minutes before the break and what a good goal it was. The ball was played forward by the North End backline into the feet of Beavon on the edge of the ‘D’. He held the ball up and played it in behind McManus, timing it to perfection for the run from midfield by Jack King, who coolly took a touch and slotted past Leutwiler into the bottom left hand corner.
The second half saw the wind and the rain step up a level.
But on 52 minutes a great chance was spurned as North End worked the ball down the left and eventually out to Stuart Beavon who crossed to David Amoo ten yards out, but he directed his header over the bar rather than under it.
The crowd was really up and North End pressed harder with Byrom flashing a show wide from 25 yards, but the visitors were still a threat on the counter attack.
The wing play from North End was causing plenty of problems and Monakana set up Laird for a chance that flashed just past the left hand post on 60 minutes.
However, the two goal lead was restored completely against the run of play moments later as the ball was poked home by Richard Smallwood after the ball wasn't cleared by the Lilywhites.
This goal took the wind out of the sails of the crowd and the Lilywhites, whose high tempo play before the goal had enlivened the stadium.
With exactly 20 minutes left the tempo was raised again as Leutwiler saved twice, once from a King header and then Stuart Beavon on the rebound, as the rain got harder and harder.
Massive pressure from North End came with ten minutes to go as Jayson Leutwiler made two brilliant saves to deny Hayhurst and then Laird as North End threw caution to the wind in an attempt to get back in the tie.
North End continued to press to try and get back into the tie, Wroe making a fine run into the box only to be denied by an excellent tackle by Parnaby as he was about to pull the trigger and then Stuart Beavon, a work horse and worthy recipient of the man of the match, forcing Leutwiler to make a fine save with a 25 yard effort.
Then with the board being held up for four minutes of stoppage time Leutwiler spilled a Laird shot and Hayhurst was stood five yards out but could only direct the ball just away, the ball eventually cleared foe a corner.
The visitors ate up the four minutes with some slow possession and progressed through the tie into the hat for the last 16.
PNE Line-Up: Simonsen, Mousinho (Procter, 86), Laird, Wroe, Huntington, Cansdell-Sherriff, Amoo, Byrom, Beavon, King (Cummins, 80), Monakana (Hayhurst, 79). Subs not used: Stuckmann, Buchanan, Welsh, Wright.
Middlesbrough Line-Up: Leutwiler, Zemmama (Haroun, 62), McManus, Bailey, Ledesma (Emnes, 63), Hines, Halliday, Arca (Thomson, 87), Parnaby, L Williams, Smallwood. Subs not used: Amougou, Jutkiewicz, Park, Ripley.
Attendance: 4,959 (446 away fans)
Referee: Mr K Stroud