Penalties put paid to county competition hopes.In the shoot out, the U's scored their first but missed their second and third penalty, meaning that Stokes was able to step up and complete a 4-2 penalty shoot-out victory for the competition holders.
And the forward made it 3-3 seven minutes before the end as he showed a striker's instinct to tuck home past Chris Lewington.
But Concord have built a reputation over the past couple of years in league and cup of never giving up and they quickly reduced the deficit to one when Stokes scored the best goal of the game with a shot from distance.
First Tyler Brampton's cross from the right hand side eluded the despairing grasp of Joe Wright, before Sammie Szmodics calmly slotted home after a Craig Eastmond cross from the right hand side.
All square at the break, the U's looked to have gained a stranglehold on the tie either side of the hour mark.
The two teams traded chances, before Concord drew level on the half hour mark. The ball was played into the box and Gary White converted from close range to level things up.
The visitors took the lead with just twelve minutes on the clock. Dom Smith knocked down a cross into the path of Macauley Bonne and he smashed home to make it 1-0.
And it was he who scored the winning penalty, after the U's missed two of their own in the shoot-out.
The U's looked well placed when they went 3-1 up with two quick fire goals around the hour mark, but Tony Stokes - prolific for Concord in his time at the club - scored a brace to level it up just before the final whistle.
Colchester United were defeated by the Essex Senior Cup holders Concord Rangers on Tuesday night, as the home side progressed via a penalty shoot-out.