But the result meant heartbreak for another Iron - with former Scunthorpe keeper Tommy Evans in goal for the Minstermen.
Former Iron transfer target Clayton Donaldson was also playing for York, in January they turned down a £250,000 bid from Glanford Park for his services.
Both Lillis and Evans were involved in the Scunthorpe side that beat Leyton Orient in the 1999 Third Division play-off final at Wembley - Evans as a player, and Lillis as assistant to manager Brian Laws.
Morecambe will face either Oxford or Exeter City in the final - Oxford hold a 1-0 advantage going into the second leg at the Kassam Stadium on Tuesday night.