The match was played at the Shimo La Tewa grounds in Mombasa, Wedensday 8 August 2012.
Mosoti Osumo opened the scoring for the champions on 38 minutes, converting a Ronald Otieno cross for the lead.
Scored late on
The second came on the 90 minute mark, with Onkundi Benson firing home to ensure victory for the Kisii based side.
The win means that Gekomoni are all but through to the semi-finals after seeing off Garissa 2-0 in their opener. They face off with Tononoka in their final match of the group and will be sure of group leadership if they avoid defeat.
St Anthony, who beat Tononoka in their opener will also look to progress as the face off with whipping boys Garissa in their final group match.
Gekomoni have six points, with Tononoka and St Anthony on three and Garissa pointless.