The home side, hosting an impressive set up at their Pardus Wealth Stadium came into the game as slight favourites despite their divisional placing in Thurlow South.
Backed with a largely welcoming but hostile support, the task for the Robins was already evident before a ball was kicked.
Harlow dominated the ball in the opening 10 minutes, as Ely stayed tight and compact from the off.
First chance did fall to the away side, as Stoker struck over from 20 yards, before the home side had an effort from a long thrown on goal, but Alfie Rogers blocked any follow up.
As the game started to open up, Harlow flexed some of their known pace on the quick synthetic surface, Alex Kerr equally as pacey had to be alert to cut off a long ball that nearly had the Harlow forward in on goal.
The game was still very tight and nervy, with niggly fouls stopping any flow to the game. Aaron Hamer was the first caution of the day as he tugged his player down although seemed to have been the one initially fouled in the lead up.
The game lacked any real quality, until Ely strung together some of the play that has seen them cut sides open all season. Louis Jenkins linked with Alex Theobold, who exchanged passes with Kerr to set Kerr off into the channel. Theobold picked up the return with his back to goal, he turned by fired just wide.
At the other end, Kerr and then Joe Brannan had to be alert to stop the pacey Harlow 7 from cutting his way through to goal, before Tyler Key saved comfortably from a header.
More little fouls were the notable events leading up to half time, as tension of a place in the final remained for both teams as they went in 0-0.
Second half started with a bang for City, as they forced back Harlow and pressed from the restart. Stoker forced a corner, which Jenkins curled in deep - Brannan rose from the penalty spot and his header looped in under the cross bar off the far post to give Ely the lead.
The next 5 minutes could have seen Ely extend their lead twice and potentially put Harlow out of sight. First, Alex Brown's left wing cross fell to Sam Tagg on the edge of the box, but his goal bound effort was brilliantly blocked by the Harlow defender. Then, almost identical to the goal, Jenkins' corner found Brannan, but this time he nodded down to Theobold who could only strike the side netting from 8 yards.
This woke Harlow up and their aggression to get back into the game was evident, as they became more direct and energised.
Their 7 again was a threat down the City right back area, he jinked his way off the line, into the box and whipped a ball across, only for Ely to clear a near tap in off the line, before Rogers blocked the follow up again.
From that following corner, the home side deservedly equalised, the tall 11 evaded his marker and smashed home after Key had saved, the crowd coming alive with cheers and an airaid siren!
Ely tried to quieten them quickly before Harlow found momentum, Kerr was seemingly shoved in the back in the area, but appeals for a penalty were waved away. Jacob Partridge then had a header just fly over from a Brown set piece. Louie Stokes, Charlie Root and Antwan Ebanks-Blake were brought on to freshen the attack, but Ebanks-Blake saw two headers sail over, as full time drew at 1-1 and we were to go to penalties.
The Robins were defeated 4-3 in the shoot-out, as Harlow were 4 for 4, with Ely unfortunately missing 2 of their 4.
Credit to the Robins, for large parts of a tight game in the spring sun - they defended well and compact, as well springing on the counter and dangerous at set pieces.
The home side offered danger throughout and use the 4G surface well when they get the ball down. They will now face their league rivals Hackney Wick who beat Thetford on penalties in the other semi-final.
Team; Tyler Key, Alex Kerr, Alex Brown, Jacob Partridge, Joe Brannan, AlfieRogers, Aaron Hamer, Sam Tagg, Louis Jenkins, Alex Theobold, Tom Stoker.
Subs; Antwan Ebanks-Blake, Louie Stokes, Charlie Root. Ash Dobson, Jevon Cook.