PNE manager Simon Grayson felt his side were worthy of at least a point at the Riverside stadium.
PNE were the better side for large chunks of the game, with a spell either side of half time being the only exception and the gaffer felt his side were unlucky in defeat.
A PNE side with five enforced changes to it started brightly in the opening half hour, but as soon as Boro took the lead through Albert Adomah, it was one way traffic at the end of the first, and the start of the second half in favour of the hosts.
However the tables turned when John Welsh and Jermaine Beckford were brought on 15 minutes into the second half with North End looking to take control of a nervous home crowd.
Despite a late onslaught from Grayson's men, Boro held on to keep their promotion hopes very much alive.
"When you look at the squad we were down to the bare bones; we've worked hard and apart from the 15 minutes after they scored, they never really hurt us too much," said Grayson to PNEPlayerHD after the final whistle.
"First half we were disciplined and kept the shape well and passed the ball well and in the second half, I don't think they really got out of their own half and we could have easily have got something out of the game which we would have deserved.
"You know they've got some good players, you look at their bench and where they are in the division and the players had to be at it and they were.
"We were lively in the first 20 minutes, they got the goal, they upped the tempo and we dropped a little bit which you can understand when they're the home team and where they are in the table but we got amongst them, but we just couldn't get the goal.
"We can be pleased with how we've performed today."
For more reaction to today's defeat, head to PNE Player via this link.