The incident happened over the Indian city of Bengaluru in Karnataka state on Tuesday.
The planes were heading straight for each other and only missed colliding by 200 vertical feet.
One plane was travelling at an altitude of 27,300 feet whilst the other was only slightly higher at 27,500 feet.
When the systems that prevented a crash came into operation, they were within five miles of each other.
The TCAS collision systems instructed the pilots to do opposite manoeuvres to escape a crash that would have been almost certainly fatal.
It is likely that one would have told to move to the left and the other to the right.
One plane had 162 passengers on board whilst the other had 166.
It is unclear what caused the planes to come so close to colliding with each other.
A spokesperson for the airline said: “The TCAS-Resolution Advisory system was triggered on two of our aircraft operating Coimbatore-Hyderabad and Bengaluru-Cochin routes, respectively, on July 10, 2-18.
“Following normal procedure this has been reported to the regulator.”
It is under investigation however by the Aircraft Accident Investigation Bureau.
They are said to be treating the incident very seriously according to India Today.
And it is not the first time the airline has found itself investigating an incident that almost resulted in a catastrophic crash.
There have been two previous near-misses in the last few months.
Both other incidents occurred in May.
Over Chennai, an IndiGo plane almost went straight into an Indian Air Force plane.
And near the Bangladeshi capital of Dhaka, another of the airlines planes missed an Air Deccan flight.