Ollie Norburn’s second half strike broke Tranmere hearts as Rovers’ hopes of visiting the new Wembley for the first time went up in smoke.
A win against Macclesfield at Prenton Park would have seen the side through to the FA Trophy final following a 1-1 draw in the first leg seven days earlier.
It has been a long wait for any glory for the club, who have suffered three relegations since their last appearance at the National Stadium back in 2000.
And that agonising hiatus goes on after the hosts struggled to stamp their authority on the game in the second half as opposition ‘keeper Scott Flinders rarely had a save to make.
Micky Mellon made three changes from Tuesday’s 0-0 draw at Torquay, with Andy Cook and James Norwood returning after being rested at Plainmoor.
The Rovers boss meanwhile also decided to switch to four at the back, having employed a 3-5-2 formation in recent weeks.
This gave his side a bit more power going forward, and also meant Adam Mekki could be accommodated on the wing without having to be shoe-horned into the side.
With the tie finely poised at 1-1 after the first leg and such a big prize awaiting the winner, nerves were always likely in the opening exchanges.
Both sets of fans created a fantastic atmosphere, with a larger than average attendance in the Kop making it quite intimidating at times for the visitors.
Rovers did see plenty of the ball without creating too many chances, with Connor Jennings particularly busy from his attacking midfield position.
One sweeping ball out to the right for Lee Vaughan culminated in a low drive by Jay Harris which was saved, before he clipped another shot over from Jeff Hughes’ short corner.
At the other end, Rhys Browne had Macclesfield’s first effort with 16 minutes on the clock, but he dragged ambitiously wide from 25-yards.
Tranmere were having plenty of the possession, but once again found a resilient defence in front of them.
Cook was not getting much change from any aerial duels with George Pilkington, whilst Mekki and Norwood were not seeing much of the ball at all.
That meant few chances were created in the first 30 minutes, with neither ‘keeper particularly stretched.
Norwood finally got a shooting opportunity just before half time though as he was released by Mekki following a quick counter attack.
The striker carried the ball into the area but after skipping past one tackle, his fierce shot was saved at the near post.
The two combined again in first half injury time, but Scott Flinders once again came out on top as he acrobatically tipped away Norwood’s curling effort from 20-yards.
Macclesfield were the much better team immediately after the break as they piled the pressure on the Tranmere goal.
Rovers had Harris to thank for an essential tackle which prevented a shooting chance whilst Andy Halls slapped needlessly off target from 40-yards.
Harris then had some space at other end as he tried his luck from distance, but his powerful effort was straight at Flinders.
The Silkmen then had their best chance yet as a quick counter attack saw the ball find its way to Ollie Norburn in the penalty area, and he rattled the bar with Davies beaten.
The midfielder was presented with another opportunity shortly afterwards though, and this time he made no mistake.
The 24-year old, who also scored in the first leg, beat Steve McNulty to bring down a long ball and immediately thrashed across goal and in at the far post, leaving Davies with no chance.
Chris Holroyd then nearly doubled the lead, running on to a sweeping pass out to the left before cutting in side and seeing his shot tipped away.
From the resulting corner, Pilkington rattled the post with a booming header.
Micky Mellon’s reaction was to bring on Andy Mangan as Tranmere threw on an extra striker, but that was countered by Macclesfield who brought on an extra defender.
Their tactics for the rest of the game were clear. They had the lead and were happy to sit back and defend it, whilst looking to hit the hosts on the counter.
Rovers meanwhile were just throwing the ball long and hoping something would bounce after Cook and find its way to a man in a white shirt.
McCombe was winning everything in the air though and even deep into injury time Tranmere struggled to get out of their own half as Macclesfield expertly showed them how to see a game out.