Tusker took the lead in the 13th minute when Timothy Otieno and Boniface Muchiri combined magnificently just outside Chemelil box before the former Gor Mahia star laid the final ball for Muchiri to tap in.
Muchiri was also on target in the first leg meeting at Ruaraka when he scored in the 41st minute to hand Tusker an eventual 2-1 win.
Lucas Waithera scored the equalizer for the sugar millers after Tusker goalkeeper Robert Mboya failed to deal with a free-kick that was delivered by George Mutimba from outside the 12-yard area.
The Millers then scored the second, that turned out to be the winning goal, in the 40th minute after Musa Ounda stepped up to convert from the penalty spot.