England's others goalscorers were Emile Heskey (7 mins) and Frank Lampard (82mins).
United keeper Ben Foster played in goal for England for the whole of the second half whilst midfielder Michael Carrick made a final 15 minutes substitute appearance.
Rio Ferdinand had earlier in the day been ruled out of the team after picking up a back injury in training.
England: James (Foster 46), Johnson, Upson, Terry, Ashley Cole, Lennon (Beckham 46), Lampard, Barry, Gerrard (Downing, 46), Heskey (Carlton Cole 15), Rooney, Carlton Cole (Crouch 34), Crouch (Carrick 75).
Subs Not Used: Green, Jagielka, Lescott, Baines.
Goals: Heskey 7, Rooney 70, Lampard 82, Rooney 90.
Slovakia: Senecky, Pekarik, Valachovic, Skrtel, Cech (Jendrisek 46), Sestak (Jakubko 72), Zabavnik, Karhan (Strba 83), Kozak (Sapara 62), Hamsik (Mintal 79), Vittek (Holosko 46).
Subs Not Used: Mucha, Cisovsky, Kratochvil, Dobrotka, Obzera, Kamenar.
Elsewhere on Saturday afternoon, United centre-back Jonny Evans scored Northern Ireland's second goal in their 3-2 win against Poland in a World Cup qualifying game in Belfast.
Evans completed the full ninety minutes for Nigel Worthington's side.
Northern Ireland: Taylor, McAuley, Craigan, Hughes, Evans, Johnson, Clingan, McCann, Brunt, Healy, Feeney. Subs: Mannus, McGivern, Baird, McGinn, Shiels, Ward, Little.
Poland: Boruc, Wasilewski, Dudka, Zewlakow, Wawrzyniak, Mariusz Lewandowski, Roger, Krzynowek, Bandrowski, Robert Lewandowski, Jelen. Subs: Zaluska, Bosacki, Wojtkowiak, Boguski, Saganowski, Blaszczykowski, Tralka.