Jacob Wright’s spot kick in the 98th minute finally gave City a deserved lead after Wilkinson’s side failed to capitalise on a handful of opportunities in 90 minutes.
Justin Oboavwoduo’s strike a few minutes later then sealed a 2-0 win at Rush Green to see City advance to the fifth round and a home tie with Reading.
And reflecting on Friday night’s dramatic victory, Wilkinson revealed that he felt it would be one of the hardest and most demanding games of the campaign for his squad.
“We’ve been together before as a group so I think we have a really good understanding of the players and what I ask of them,” said the head coach.
“And the players have been top over the past 48 hours and you could see once we got together that it is a competition they are desperate to do well in.
“Their desire and application over the past couple of days shines through. They gave us everything on the night and I don’t think we’ll face many games as difficult as that.”
Elite Development Squad players Jacob Wright, Joel Ndala, Justin Oboavwoduo and Michael Okeke featured in their first FA Youth Cup game of the campaign alongside Jahmai Simpson-Pusey, Lakyle Samuel and True Grant who all featured in City’s 2-0 third round win over Watford in December.
And they all proved to be key figures in City’s hard fought win at both ends of the pitch with the side’s defensive heroics matched by energy in the attacking third.
“We knew it was going to be a difficult game. Obviously they won the competition last year, we faced them in the national final last year and they are top of the southern league this year,” added Wilkinson.
“The pitch made it tricky for us to get any sort of rhythm into our game in the first half so I think that’s exactly what we expected and we knew it was going to be a battle but I thought the lads stood up really well in terms of their character.
“Once we got in at half time and reorganised our attacking shape, I thought we looked a lot better in the second half in terms of how we found the space and the longer the game went I thought we were going to be the team to score first.”
With the holders now out of the competition, City remain focused on eclipsing last season’s efforts which saw us reach the semi-final.
However, the head coach said he was looking to take the FA Youth Cup game by game.
“For us, like anyone, we just want to focus on Reading,” added Wilkinson.
“They had a good away result against Sheffield Wednesday this week but, of course, when you look at a competition like this the top teams are always going to be there or thereabouts.
We all know who they are and are going to take some beating.”