After drawing 2-2 with Pompey's youngsters after 90 minutes, Colchester booked their place against City in the grand final by winning 5-4 on penalties.
The Bantams secured their spot in the cup decider after defeating Hull City in the northern section final at the Coral Windows Stadum last Saturday.
City will go for glory in the Youth Alliance Cup Final having already secured the Youth Alliance (North East) Division title late last month.
A venue and date for City's final with Colchester are to be confirmed.