Jared Omwenga scored the lone goal of the game in the first half to land the visitors three crucial points at the Awendo Green Stadium in South Nyanza.
Chemelil were the better side on the day and fully deserved the win.
Omwenga scored on 43 minutes, slotting home the rebound after SoNy keeper Victor Oduor parried his own shot.
Otherwise, the first half was dominated by missed chances for SoNy, with Ismael Dunga, and Francis Ocholla the culprits.
At the other end, Tonney Opondo could have easily had three goals as he also missed a succession of chances on goal.
Hit the bar
SoNy improved in the second half but still could not find the elusive goal.
Dunga was again in the midst of the action, as he shot wide and over the bar in two chances within three minutes of each other.
Omwenga too could have added a second but he hit the bar from close range.
At the death, Dunga had two other chances to score, first swiveling and posting wide and then in added time, he hit the crossbar when it looked easier to score than miss.
On reflection, SoNy were second best as Chemelil looked dangerous and could have scored as many goals as they like.
Chemelil overtake SoNy in the standings with the victory.