Paul Mucureezi could have opened the score in the 28th minute but he sent his effort over the bar after he had been put through on goal by Disan Galiwango.
A minute after the half-hour mark, Murushid Juuko was booked after he exchanged words with referee Ssali Mashoodi.
Mucureezi was unlucky in the 35th minute when his second chance went narrowly wide after receiving a cross from Karim Watambala.
Watambala was the culprit in the 41st minute when he wasted another chance after Bbosi Byarughanga produced a good cross for him.
Eric Kambale s 42nd-minute header - from a cross by Godfrey Lwesibwa - went over the bar as Express mounted more attacks against the hosts.
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Vianne Ssekajugo and Joshua Lubwama, both of Wakiso Giants, saw their chances go wide as well. As the second half began, Solomon Okwalinga was unable to give Mbarara City an opener as his effort went wide from a clever position.
Uganda international Ssekajugo would have opened the score in the 55th minute as his effort was ruled out for offside. Two minutes after Ssekajugo was flagged down, the Purple Sharks took the lead as Atuheire - who received a good cross from Owen Kasule - opened his goal account.
Jude Ssemugabi wasted a chance to make the score 1-1 when his penalty hit the crossbar. The penalty miss helped Wakiso Giants move up to the eighth position after picking up draws in the previous five games.
We are very pleased following our second game here in Cameroon after what was a very positive performance against the host Nation a few days ago with 10 men, McKinstry said after the win. We decided to basically change everybody in the team. We made 10 changes in the starting lineup but maintained one in Tonny Mawejje and that was purely to make sure the midfield had the right balance. We knew before the game that he would come out at half-time and Shafik Kagimu would come in. We knew what substitutes would be made. The players knew what would happen at half time. Overall, I thought that the 10 players who came in put up a good performance.