CK Vineeth scored the opening goal of the match in the 50th minute and Anirudh Thapa doubled the lead for Chennaiyin in the 58th minute as the Marina Machans sealed their place in the final.
Eugenson Lyngdoh replaced the suspended Pronay Halder in midfield and Edu Garcia returned after missing out on ATK's 4-3 win over Delhi Dynamos in the quarterfinal.
Jeje Lalpekhlua was dropped to the bench as CK Vineeth led the line. John Gregory opted for an extra foreigner in Chris Herd and Jerry Lalrinzuala made his first appearance this calendar year.
Manuel Lanzarote and Lyngdoh tried their luck from long-range in the opening minutes. At the other end, Vineeth failed to tap in on the near side from Lalrinzuala's low cross as early as the fifth minute.
ATK did have another chance through Jayesh Rane, whose shot was blocked by Chris Herd inside the box.
Chennaiyin peppered the ATK backline with numerous crosses but a finish was severely lacking. Anirudh Thapa had the easiest of chances from one such cross from Gregory Nelson but the India international squandered the opportunity. The only shot on target of the first half was a Balwant Singh effort from 40 yards out.
Thapa made up for his earlier blemish as he created the first and scored the winner within an eight-minute period.
The 21-year-old went past John Johnson to send a cross into the box for Vineeth. The on-loan Kerala Blasters striker leapt over Ricky Lallawmawma and headed in the opener of the night.
In the 58th minute, Laldinliana Renthlei squared the ball to Nelson who released a diagonal for Thapa and the young midfielder drilled it into the net.
In the final quarter of an hour, Karanjit Singh had to make two crucial saves to see his side through. After a one-two with Hitesh Sharma, Lyngdoh's effort deflected off Thapa and was going in but the goalkeeper kept it out. The custodian also denied Lanzarote from a freekick.
Substitute Thoi Singh could have added a third for the Chennai side but his shot grazed the outer side-netting.
John Gregory's side will now play out a repeat of the 2015 Indian Super League final as both Goa and Chennaiyin look to win their maiden Super Cup on Saturday.