Dhoni, ranked 52nd in the chart, was the only Indian sportsperson to make the list which also included four of his compatriots in "Titan of Industry" Mukesh Ambani (61), "Brain Mapper" VS Ramachandran (79), "Philanthropist" Azim Premji (88) and "Change Agent" Aruna Roy (89).
Dhoni found himself way above Messi who was just below Obama at the 87th spot in a list topped by Wael Ghonim, the Google executive who became the "Spokesman for a Revolution" in Egypt.
The 29-year-old Dhoni, who has 2,925 runs in 54 Tests and 6,049 runs in 186 one-dayers, is the most successful Indian cricket captain under whom the team also won the inaugural Twenty20 World Championship in 2007.
The magazine described Dhoni as "captain fantastic".
"Dhoni is now universally acknowledged as India's best captain ever. He's also its most likable, exuding both cool confidence and down-to-earth humility.
"As astonishing as Dhoni's talent is his background.
"Indian success stories are usually associated with pedigree, connections and power. Dhoni, from a small-town family of modest means, had none of these but he's shown India that you can make it with only one thing: excellence," read the accompanying profile penned by acclaimed author Chetan Bhagat.
"Dhoni doesn't just lead a cricket team, he's also India's captain of hope. And he didn't just win India the World Cup, he also taught India how to win."
Dhoni, the highest-ranked Indian in the latest Time Magazine 100, is only the second Indian sportsman after Sachin Tendulkar to make the prestigious list.
The others global celebrities included in the list are US Secretary of State Hillary Clinton, who is incidentally ranked higher than Obama at 43rd, Facebook founder Mark Zuckerberg (6), and Wikileaks founder Julian Assange (9).