Although United dominated the game, several first-half chances were either spurned, or denied by Stoke's agile goalkeeper Paul Cooper.
Stoke could have twice taken the lead. The Reds were grateful to goalkeeper Dermot Mee for at least one vital save, while right-back Iestyn Hughes demonstrated his determination with an excellent recovery tackle.
Those interventions by the visitors ensured the game remained goalless until the final minutes, giving United the platform to go on and make it three wins from three in November.
Reds centre-back Bjorn Hardley was credited with the assist, a long switch of play that sent his fellow Dutchman clear to find the net. Hoogewerf, a 69th-minute replacement for Charlie McNeill, controlled the ball with a fine first touch before beating Cooper finally with an emphatic finish.
Former NAC Breda junior Hardley was snapped up by United last year.