A five-wicket win in the third game of the five-match series on Sunday gave India an unassailable 3-0 lead over Steve Smith's Australia.
It also stretched India's winning streak to a record 12 matches across all formats.
Kohli's side have been on a roll for the past year since regaining the number one Test spot with a 3-0 home whitewash of New Zealand.
The in-form captain has led from the front with 1,137 runs in 21 50-over matches this year, ahead South Africa's Faf du Plessis as the highest one-day scorer in 2017.
Kohli praised his team after the latest win against the once mighty Australians, who have been outplayed in India. Smith's team also lost a Test series 2-1 in India this year.
"Credit to the whole squad for the series win, but the journey stops only after the final game," said Kohli, the top ODI and T20 batsman in the International Cricket Council (ICC) ratings.
"We may give opportunities for people from now, but all 15 guys know that we got to be ruthless once we step onto the field," Kohli added.
The series has seen new Indian stars emerge, with all-rounder Hardik Pandya and left-arm wrist spinner Kuldeep Yadav making an instant impact.
While Pandya's crucial 78 led the team's run chase in Indore, Yadav impressed with his maiden hat-trick in the second international.
However legendary spinner Bishan Singh Bedi believes India have not been tested by opposition teams, barring the Champions Trophy final in June against Pakistan which they lost by 180 runs.
India won 10 of their 13 Tests on home soil in the 2016-17 season and then went on to rout hosts Sri Lanka over nine games in all three formats.
"Realistically speaking Indians are not even fielding their best XI and beating the opposition hands down, whether it is Sri Lanka or Australia," Bedi said.
"We are loving the ratings, but if we are a little more pragmatic then you will realise that the Indian team in the last year or so haven't been stretched by the opposition.
"Just that one game in the Champions Trophy final against Pakistan, other than that we have not seen them in a tight situation.
"We will get to know the character of the team when they come out of a tight situation," Bedi added.
Left-arm spinner Axar Patel returns to the Indian squad in place of Ravindra Jadeja for the final two ODIs that will be played in Bangalore and Nagpur on Thursday and Sunday.
Patel, who sprained his ankle at the start of the series, will join Chahal and Yadav as the third spinner in the 15-man squad.
