After the series victory, ICC tweeted the updated the list on social media with Team India leading with 124 runs, three points ahead of New Zealand.
Jasprit Bumrah had bowled Ollie Pope and Jonny Bairstow in a sensational spell of reverse swing that tilted the game decisively in India's favour and helped the visitors take a 2-1 lead in the five-match series.
Root had started the series in the fifth position but his 507 runs in three Tests have helped him overtake Kohli, Marnus Labuschagne, Steve Smith and finally New Zealand captain Kane Williamson, whom he now leads by 15 rating points.
Jadeja returns to the top spot in the ICC Test Rankings dethroning Windies star, Jason Holder.
Steve Smith, who claimed the top spot for the first time since the Boxing Day Tests last year, takes over from New Zealand captain Kane Williamson, who is set to lead his team in the WTC final.
Nepal's Khushal, on the other hand, was the leading run-scorer as his team won a tri-series also featuring the Netherlands and Malaysia
Babar has emulated compatriots Zaheer Abbas - 1983-84, Javed Miandad - 1988-89, and Mohammad Yousuf - 2003 - as the number one ODI batsman.
Bhuvneshwar Kumar, who made his international comeback with England series moved up to 11th from 20th in the ICC ODI rankings for bowlers.
India opener Shafali Verma continues to be the top ranked batter in the ICC T20I Player rankings after the blistering 30-ball 60 in the final match of the home series against South Africa helped her garner 26 rating points.
In the T20I rankings, KL Rahul dropped to the fifth spot after an underwhelming show in the recently concluded five-match series.