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 custodian 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.
Chemelil Sugar picked a point against Bandari FC in their previous match at home, following a goalless draw. On the other end, Tusker registered a 3-1 win over visiting Kariobangi Sharks and were keen to extend their good away form.
Chemelil Sugar will now face AFC Leopards at the same ground on April 3 as they try to race away from the relegation zone.
Chemelil Sugar XI: Alube Morgan, Opondo Chrispin, Mahiga Vincent, Mwangale Philiph, Odhiambo Jacob, Akoko Nicholas, Okiya Charles, Oundo Musa, Waitere Lucas, Ochieng John, Mutimba George.
Subs: Onunga Bernard, Otieno Bravo, Omino James, Kibet Gideon, Erick Juma, Wangulu Gilbert and Muchuma Philip.
Tusker XI: Robert Mboya, Eric Ambunya, Hillary Wandera, Justine Omary, Brian Odhiambo, Faraj Ominde ( Peter Nzuki), Jackson Macharia, Sydney Ochieng (John Kamau), Clyde Senaji (Amini Muzerwa) and Timothy Otieno.
Subs: Omondi, Meja, Tangauzi, Madoya.