Manukau barely looked like scoring before the break, but had the better of much of the second half as the hosts appeared intent on protecting their advantage.
The dangerous Tadeu Castro brought Manukau level in the 53rd minute with a nicely taken strike after United defenders hung off him in the box, before Andrew Cooper earned his side a penalty with a nifty touch that wrong-footed his marker.
McNab converted into the bottom left corner, but Manukau was back on level terms six minutes later when United goalkeeper Tom Pamment dived over the top of a Castro free-kick from just outside the area.
Manukau finished the stronger, but it was United that produced the better chances at the end of regulation.
McNab missed badly from the spot before Hughes had a goal awarded, then rubbed out, for hand ball in the final seconds of injury time.
Extra time began poorly for United with the exit of a demonstrative and shirtless Mark van der Salm following a studs up 50-50 challenge in which he appeared to make first contact with the ball.
Hughes' classy finish made it 3-2 despite the numerical disadvantage, but this time the lead lasted just three minutes as Leo Berlim nudged home a sitter after Pamment essentially ran right past what should have been a routine clearance.
McNab earned his side's third penalty with a clever touch past goalkeeper Faizal Hanif, which Hughes calmly slotted to make it 4-3.
That is how it stayed, with the committed 10-man United side playing cleverly into the corners to wind the clock down.
Coach Duncan Lowry bemoaned the large number of missed chances, but was proud of the effort of his players ahead of their top of the table league clash away to Fencibles United on Saturday.
Tauranga City United 4 (Sam O'Reagan, Jack McNab, Jerahl Hughes 2) Manukau City AFC 3 (Tadeu Castro 2, Leo Berlim)