Molyneux came off the bench and made an instant impact to draw Pools level with a stunning strike from the edge of the area and force a penalty shootout.
Pools had taken the lead through Joe Grey’s clever chipped finish early in the first half but fell behind after Mason Burstow’s equaliser was added to by Alex Gilbey.
But Pools took the game to the League One side in the second half and got their reward as Molyneux curled in delightfully.
And with neither side able to find a winner it meant penalties would be required to decide the tie with fullback Jamie Sterry the man to send Pools into the semi-final.
“It’s the best way to win a game. It was nerve-racking but I think we deserved it in the end,” said Molyneux.
“He just said to go on and make a difference. I think I started running off celebrating before it even hit the back of the net to be honest.
“But I feel like I need to do that a lot more often and be consistent with it.”
Pools will now face either Rotherham United, Wigan Athletic or Sutton United in the semi-finals with Lee’s side just 90 minutes from a Wembley final and Molyneux believes Pools will have no fear if they are drawn against another League One side.
“We just play with no fear. And the lads enjoy their football when we’re the underdogs and we just battle to the end.”