"A girl who has just won the world isn't going to be upset over a tongue-in-cheek remark. 'Chillar' talk is just small change - let's not forget the 'chill' within Chhillar," Manushi tweeted, and tagged Tharoor as well as Times Group Managing Director Vineet Jain.
Manushi, a medical student from Haryana, won the title in China, ending 16 years of drought for India at the international beauty pageant.
After her victory, Tharoor had tweeted: "What a mistake to demonetise our currency! BJP should have realised that Indian cash dominates the globe: look, even our Chhillar has become Miss World!"
This post didn't go down too well with some social media users who pointed out there is a difference between Manushi's surname "Chhillar" and the word "Chillar" - in spelling and meaning.
Later, Tharoor took to his social media pages and asked people to chill.
"Guess the pun is the lowest form of humour, and the bilingual pun lower still! Apologies to the many who seem to have been righteously offended by a light-hearted tweet today. Certainly no offence was meant to a bright young girl whose answer I've separately praised. Please: Chill!"
Manushi's reaction on the issue came on Monday in response to a post by Jain of Times Group, organisers of the Miss India contest.
"I saw Shashi Tharoor's tweet regarding Manushi Chhillar. I wasn't offended even though she is a Times girl. We need to learn to be more tolerant towards light-hearted humour."
Manushi is the sixth Indian to win the Miss World pageant after Priyanka Chopra brought the crown in 2000.