Stars wasted no time stamping their authority on the tie with the first goal through Harris Tchilimbou in the opening 45 seconds at Moses Mabhida Stadium.
Chiefs, obviously rattled, looked for a quick response after Joseph Molangone played in Ryan Moon, who headed wide.
Molangoane then decided to go for goal himself and went one-on-one with Thela Ngobeni but the latter came out trumps with a good save after 11 minutes.
Those chances came back to haunt Amakhosi as they conceded yet again with Tchilimbou sneaking in behind the defence to finish off from close range after 34 minutes.
This forced Steve Komphela into an early change, bringing on Dumisani Zuma for Philani Zulu as he went all out attack, given their circumstances.
A header at the back-post from Zimbabwean Willard Katsande was the closest they came from reducing the score-line heading into the break.
Komphela brought in another player from the bench, with Leonardo Castro replacing Tsepo Masilela at the start of the second half.
It did nothing to stop Ea Llo Koto from continuing to get on the front foot after Sinethemba Jantjie shot wide from a breakthrough into the box.
Substitute Castro missed a glorious opportunity to cut the deficit in half after directing a free header way off target in the 53rd minute.
Hendrick Ekstein came close to getting on the score-sheet himself, but excellent goalkeeping from Ngobeni thwarted his attempts.
Stars were not content sitting back, despite their two-goal lead, and Siphelele Mthembu went close to exerting more damage on his former club but a good save from Khune kept him out.
That was all it came down to in the end, with Stars walking away victorious for their first cup final since December 1999.