Kenny Jackett's troops were handed a clash against their League One rivals at Molineux, as the second-round draw was made live on Soccer AM.
Holders Crewe continue their defence with a trip to Highbury Stadium, while Bristol City's reward for their derby win over Rovers is a meeting with Wycombe.
Other stand-out ties see Sheffield United host Hartlepool, Preston tackle Oldham, Peterborough taking on Brentford, and Leyton Orient going head to head with Coventry.
Johnstone's Paint Trophy second-round draw:
York v Rotherham; Sheffield United v Hartlepool; Wolves v Notts C; Mansfield v Chesterfield; Fleetwood v Crewe; Morecambe v Carlisle; Preston v Oldham; Port Vale v Rochdale.
Southend v Dagenham & Redbridge; Peterborough v Brentford; Stevenage v MK Dons; Leyton Orient v Coventry; Oxford v Portsmouth; Swindon v Plymouth; Wycombe v Bristol City; Crawley v Newport.
Ties to be played on week commencing Monday 7 October.