The teenager waited until the City players had left the bus before making his move, which came just days after Swansea ball boy Charlie Morgan was kicked by Chelsea forward Eden Hazard.
Stoke's culprit was banished to the stand.
Meanwhile, Rafa Benitez claimed Chelsea will appeal if the FA's independent regulatory commission increases Hazard's suspension.
The £32million Chelsea star has until 6pm on Tuesday to respond to an FA charge.
Hazard is already serving a three match ban, which started in Sunday's FA Cup tie at Brentford, but the FA want the punishment increased.
Charlie Morgan, 17, the ball boy wrapped up in contraversy after he was kicked by Chelsea star Eden Hazard has been banned from next month’s Wales international against Austria, the Sunday People has reported.
Morgan, could have been one of 16 lads from Swansea youth team Union Rangers sent as ballboys to the friendly at the city’s Liberty Stadium. But Football Association of Wales chiefs insisted he must not go.
Swansea City chief Martin Morgan: “He’s portrayed as a spoilt nancy boy but it couldn’t be further from the truth.”
Charlie shook hands with Hazard after the 0-0 draw took the Swans to the final. But Hazard now faces an FA ban.