Rooney grabbed the vital goal with 17 minutes left after being set up by Cristiano Ronaldo.
The late strike capped a fine tournament for Rooney who had scored twice after coming off the substitute's bench in Thursday's 5-3 semi-final victory against Asian champions Gamba Osaka.
But Sunday's win was marred by Nemanja Vidic's dismissal in the opening stages of the second half when the Serbia international aimed an elbow at Claudio Bieler as the two men lay on the ground.
United had dominated the goalless opening half but would have led at the interval but for some superb goalkeeping by the Ecuador team's veteran shot-stopper Jose Cevallos.
However, Quito created the first opening of the match when Jairo Campos somehow failed to find the target after getting on the end of Alejandro Manso's free-kick.
When United responded, Cevallos twice denied Rooney before diving to his right to keep out Carlos Tevez's header after some good work by Ronaldo.
Cevallos then palmed away Park Ji Sung's fierce shot before keeping another Tevez effort out.
Park sliced an attempted chip over the bar just before half-time as United continued to dominate.
However, the second half was a more even affair after Vidic's dismissal which looks set to keep him out of at least the first Champions League clash with Internazionale in February.
Manso tested Edwin van der Sar with a long-range effort but it was United that finally broke the deadlock in the 73rd minute when Ronaldo set up England international Rooney who fired a crisp shot into the far corner of the net.
The South American champions tried hard to grab a late equaliser with Manso going closest with another rasping long-range drive that Van der Sar was forced to tip over the bar.
Liga Deportiva : Cevallos, Norberto Araujo, Calle (Ambrossi 77), Campos, Calderon, Reasco (Larrea 82), Urrutia, William Araujo, Manso, Luis Bolanos (Navia 87), Bieler.
Subs Not Used: Dominguez, Obregon, Delgado, Eder Vaca, Danny Vaca, Chango, Viteri.
Booked: Bieler, Campos, Cevallos, Calle, William Araujo.
Man Utd: Van der Sar, Rafael Da Silva (Neville 85), Ferdinand, Vidic, Evra, Ronaldo, Carrick, Anderson (Fletcher 87), Park, Tevez (Evans 51), Rooney.
Subs Not Used: Kuszczak, Berbatov, Giggs, Nani, Scholes, Welbeck, O'Shea, Gibson, Amos.
Sent Off: Vidic (49).
Booked: Anderson.
Goals: Rooney 73.
Att: 62,619
Ref: Ravshan Irmatov (Uzbekistan).