The chilli is not native to India. It arrived from the Americas via Portuguese traders around 1498-1510. Within 200 years it had replaced black pepper as India's primary heat source. One of the fastest and most complete ingredient adoptions in culinary history.
Before the chilli arrived, India's heat came from black pepper (Piper nigrum), long pepper (Piper longum), ginger, and asafoetida. The Arthashastra (4th century BCE) and Ayurvedic texts describe these as the primary pungent agents. The original black pepper of the Kerala Ghats was one of the most valuable commodities in world trade — the spice that drove the Europeans to find a sea route to India. When Vasco da Gama arrived in Calicut in 1498, the black pepper trade was what he came for.
The chilli arrived with the Portuguese who came after Vasco da Gama — a Capsicum annuum or Capsicum frutescens from the Americas, which had reached Portugal through the Spanish colonial network. The Portuguese planted it in their coastal settlements (Goa, Calicut, Cochin) and it spread inland with remarkable speed.

The chilli's adoption into Indian cooking was one of the fastest ingredient adoptions in culinary history. The reasons are practical: chillies grow easily in India's climate (they thrive in the same conditions as many native crops); they are cheaper to produce than black pepper (which requires specific growing conditions and complex harvesting); and they provide more consistent, controllable heat. Black pepper heat is warm and diffuse; chilli heat is sharp and immediate — and in cooking, the immediate heat was more useful for certain preparations. The economics and the culinary utility both favoured the chilli.