The US-listed company, which has a large portion of its 1.63 lakh workforce in India, paid Mr D'Souza a base salary of $590,000, stock awards worth $9.59 million and a non-equity incentive plan compensation of $405,780 for the last year.
However, his $10.61 million package for 2012 was lower than $11.76 million paid to him in 2011 when 44-year old Frank had got stock awards of over ten million dollars.
Frank is credited with expanding Cognizant's annual revenue from $1.4 billion to over $7 billion in last six years and has led the company to deliver industry-leading growth in a tough business environment.
Despite a decline from the last year's level, Frank's $10.61 million pay package is the highest among all the top executives of the company.
Cognizant President Gordon J Coburn received $6.23 million, while others with significant pay packages included Rajeev Mehta ($5.19 million), Ramakrishnan Chandrasekaran ($3.62 million), Karen McLoughlin ($2.5 million) and Malcolm Frank ($2.49 million).
Mr D'Souza, an MBA from Carnegie-Mellon University, was appointed Cognizant CEO and became a member of its Board with effect from January 1, 2007. Son of an Indian diplomat, he had joined Cognizant as a co-founder in 1994 -- the year it was started as a division of The Dun & Bradstreet Corporation.
With over 50 delivery centres worldwide, Cognizant is a member of the US stock market benchmark indices like NASDAQ-100 and the S&P 500, while the company also figures among the lists like Fortune 500.
It has overtaken Indian giants like Infosys and Wipro in terms of IT service revenues.