It was Liam Craig who put Ipswich ahead in the 8th minute and it wasn't until injury time of the second half that City grabbed the equaliser. Francino Francis made it 1-1.
The referee then judged a handball in the penalty area against Stoke's youngsters and Liam Craig took up the opportunity to score the winning goal, his second of the night.
Ipswich now face either Aston Villa or Port Vale u18s.