A brace from Isaac Ogwang and Derrick Ndahiro penalty put Villa in third with four points after two games.
Ndahiro scored from the spot in the 10th minute before Ogwang doubled the lead in the 20th.
Ogwang picked his brace in the 37th minute when he directed a header off Goffin Oyirwoth’s cross.
It could have been worse, but Ndahiro missed his second penalty in the 70th minute after Pistis Barenge was wrongly judged to have handled the ball in the area.
The sixteen time champions have now won four successive home games against the Ankole Lions.
In the second half, Mbarara City put up a better challenge with former SC Villa forward Bashir Mutanda coming close but the Jogoos defended resolutely.
SC Villa move third on the table with four points in two games, two points adrift of leaders KCCA FC.
SC Villa XI– Meddie Kibirige, Fred Agandu, Derrick Ndahiro, Gavin Kizito, Asuman Alishe, Amir Kakomo, Goffin Oyirwoth, Emmanuel Wasswa, Ronald Ssekiganda, Nicholas Kabonge.
Subs – Martin Ssenkooto, Fahad Badiro, Moses Kiggundu, Faizal Muwawu, Abdallah Ssekandi, Abdullah Salim, Muhammad Nsereko
Mbarara City FC XI – Mohammad Ssekeba, Steven Othieno, Jasper Aheebwa, Hilary Mukundane, Bamba Souleymane, Pistis Barenge, Solomon Okwalinga, Raymond Onyai, Ibrahim Magandazi, Bashir Mutanda, Salim Huud
Subs – Opio Jackson, John Adriko, Karim Ramathan, Ivan Eyam, Edwok Ronald, Ronald Otti, Oyirwoth
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Next match for both teams
Another Result on Wednesday, December 9
Kitara FC 1-5 UPDF FC