Bektur Talgat (22', 82' and 84' 90+'), Ansumana Kromah (67') and Brandon Fernandes (90') found the net for Churchill while Michael Soosairaj scored for the Southerners in the 54th minute but it went in vain.
Keenan Almeida and Rowilson Rodrigues returned from suspension and injury respectively to slot in place of Meldon D'Silva and Fulganco Cardozo as Derrick Pereira started with his full strength first XI.
The away coach V. Soundararajan was without the services of Debabrata Roy and Denson Devadas while Abhishek Das was shifted to the bench as Joseph Clemente, Raju Yumnam and Zakeer Mundampara made their way in.
After a drab start, Churchill took the lead after Bektur found himself in the right place at the right time to slot the loose ball at the back of the net following a goalmouth melee from Brandon Fernandes' flag kick in the 22nd minute.
At around the half-hour mark, Ansumana Kromah's shot took a deflection off a defender after Brandon cut the ball back for the Liberian from the touchline, besides another good attempt by Anthony Wolfe from the edge of the box towards the end of the half, though Karanjit Singh punched it out and the corner was interrupted by a foul by Bektur.
The two opportunities that befell the hosts was sandwiched by a snapshot by Chennai City's Edwin Vanspaul who went for the far post from the right, which missed the target.
Just before half-time, Wolfe put in an inch-perfect cross from the right but Richard Costa was unable to tap it in as he missed it altogether.
After a flab shot by Dhanpal Ganesh wasn't enough to threaten Naveen Kumar, the Churchill goalkeeper was completely beaten to Soosairaj's excellently executed left-footer from just inside the box that curled into the top left corner of the goal a short pass from Mundampara in the 54th minute.
Referee Ranjit Bakshi was brave enough to flash the second yellow card to Anyichie, who was earlier booked for a foul on Brandon, for a shameful handball by the Nigerian defender which prevented Kromah from receiving the pass in the 60th minute.
After continually complaining to the referee of the away side wasting time over taking their goal-kicks and setpieces, Kromah decided to take things in his own hands as he played a one-two with Brandon and slotted it past Karanjit to put Churchill back in the lead in the 67th minute.
Both sides had fair chances to score another. Churchill's attack on the counter with Kromah and Brandon on the break saw the latter's cross from the left is blocked well by Raju Yumnam in the 78th minute. In the next minute, Charles almost got to the ball after it had past Naveen but Seriton was at hand to effect the clearance after Vanspaul had lobbed the ball in the box.
Then, to extend the hosts' lead in the 82nd minute, Brandon's free-kick was tapped in by a grateful Bektur who completed his brace. The Kyrgyz midfielder went on to score the first hat-trick for Churchill Brothers this season after substitute Anthony D'Souza made an immediate impact with a cross from the left which resulted in Bektur heading the ball at the back of the net.
There was no stopping the Red Machines on the evening as Brandon took the ball into his preferred space from where the Goan midfielder drove his right-footer past Karanjit Singh from the edge of the box at the end of regulation time.
Another goal was scored off Brandon's free-kick in injury time as Bektur's header bounced awkwardly for Karanjit and the ball nestled at the back of his net once again as the night finished on a miserable note for the away side.