Also among the honourees divided into 10 categories in the issue "recognising a year of tumult, protest, inspiration, and new beginnings" released Monday are three Indian Americans.
"Each year, our list of leading Global Thinkers spotlights those who have translated their ideas into actions, impacting millions worldwide," said David Rothkopf, editor and CEO of The FP Group.
Modi is listed among the "Decision Makers" "for enthralling the world's most populous democracy", while Shah gets the honour "for engineering Modi's landslide".
Other "Decision Makers" include Germany's Chancellor Angela Merkel, and Mexico's Secretary of Finance, Luis Videgaray.
"In a year when Russia annexed Crimea, and the Islamic State redefined the very nature of terrorism, a group of Indian scientists and engineers also showed the world how to send a spacecraft to Mars on a budget," the magazine noted.
Aerospace engineer Mylswamy Annadurai, leading Indian Space Research Organisation's Mars Orbiter Mission team, is listed among the Innovators "for putting India into orbit on the cheap" and showing "that cosmic achievements don't have to break the bank".
Listed among the Chroniclers or "the masters of storytelling", is Shubhranshu Choudhary, founder of CGNet "for giving rural Indians a megaphone".
Choudhary, who left his job as a BBC producer in 2010 to launch the mobile news service CGNet Swara "beat out leaker Edward Snowden for the Google Digital Activism Award", the magazine noted.
Figuring among the Moguls is Kiran Mazumdar-Shaw
"Journalism needs to become everybody's business," he was quoted as saying when receiving the award.
Also listed among Chroniclers is India's first transgender TV anchor Padmini Prakash "for bringing third gender to prime time".
Prakash was crowned Miss Transgender India in 2009, it noted.
Figuring among the Moguls is Kiran Mazumdar-Shaw, chairperson and managing director of Biocon "for insisting that good health care shouldn't break the bank".
State Bank of India chair Arundhati Bhattacharya, who in 2014 was listed as the world's 36th most powerful woman by Forbes, makes the Moguls list "for telling hard truths about India's debt".
Indian-American researchers Partha Dasgupta and Veerabhadran Ramanathan figure in the list of Naturals "for keeping the faith in the fight against climate change".
Dasgupta works at Cambridge University while Ramanathan is at the University of California, San Diego.
Sangeeta Bhatia, an engineer and physician working at Cambridge, Massachusetts is listed among the Healers "for creating a kinder alternative to the colonoscopy".