Neil Baker named an unchanged 16 from the match at Colwyn Bay on Saturday, whilst Colne fielded five players who also started in their Lancashire FA Trophy final defeat on Monday night.
Dan Trickett-Smith had the first opportunity on 4 minutes but his shot was deflected for a corner.
However it was generally a quiet opening period until Blues took the lead in the 14th minute when Rob Stevenson latched onto a superb pass from Trickett-Smith and tucked the ball past Colne keeper Hakan Burton.
Danny Roberts was forced into a fine save four minutes later as the visitors hit back but there was nothing he could do about the equaliser on 35 minutes when Reece Weeb-Foster lashed the ball into the net with a sweet finish from the right hand side of the area.
Colne had the ball in the net again as they finished the first half strongly but it was ruled out by the assistant's offside flag.
The Lancashire side looked the more likely early in the second half and had another effort chalked off for offside following a close range finish in the 59th minute.
Leek gradually worked there way back into the game and produced a superb move down the right involving Trickett-Smith and Stevenson but the cross was just taken away from Jordan Johnson by a last-ditch challenge.
Tim Grice and Charlie Walford came on after 72 minutes and seven minutes later Grice was in on the end of a low cross but the ball was deflected out for a corner by a defenders leg.
Colne almost snatched it in the 82nd minute when an effort following a left-wing cross hit the bar.
With 90 minutes approaching the visitors were reduced to ten men when Reece Webb-Foster was shown a straight red for the use of the elbow on Jack Sanders.
The score remained 1-1 and the match went to extra-time allowing the ten men to regroup and there was little to report in the first period of extra-time as Leek struggled to create any openings against a well-organised defensive unit.
In the 111th minute a cross right across goal by Trickett-Smith found Grice at the back post but his header was cleared off the line.
However Blues record goalscorer was not to be denied and with 119 minutes on the clock. Walford swung in a corner which was headed goalwards by Darren Chadwick. The keeper pushed the ball away but it fell to Grice and he smashed it home into the roof of the net from six yards to spark wild celebrations.
Unfortunately one spectator ran onto the pitch and Colne's Waqas Azam manhandled him and was shown a red card by the referee.
There was still time for Trickett-Smith to round the keeper and with the goal gaping blast the ball over the cross bar with the last kick of a truly memorable game.
Leek go on to play Radcliffe FC at the Neuven Stadium on Saturday in the final.
1. Danny Roberts
2. Niall Green
3. Lewis Short (14. Rio Adebisi, 105)
4. Marc Grocott
5. Darren Chadwick
6. Jack Sanders
7. Niall Maguire (12. Charlie Walford, 72)
8. Billy Reeves
9. Jordan Johnson (15. Tim Grice, 72)
10. Dan Trickett-Smith
11. Rob Stevenson
Unused subs: 16.Scott Lycett, 17. Ben Chapman
Yellow Cards: Short, Chadwick, Sanders, Walford