Timothy Cook, 49, will also receive 75,000 restricted stock units scheduled to vest in 2011 and 2012, Apple said in a regulatory filing Friday.
Jobs, 55, famously limits his salary to $1 per year, which leaves Cook the company's highest-paid executive. In 2009, Cook received an $800,400 salary; $800,000 in nonstock incentive compensation; and about $40,900 in company matches to his retirement account, life insurance premiums and cash for unused vacation days.
The COO also holds 13,741 shares of Apple stock and 500,000 additional restricted stock options that have not yet vested, according to a January filing with the Securities and Exchange Commission.
Cook took the company reins when Jobs, a pancreatic cancer survivor, went on medical leave from January through June 2009.
It was Cook's second stint leading Apple. Cook, who joined Apple in 1998, ran the Cupertino, Calif.-based company for two months in 2004 while Jobs recovered from surgery for pancreatic cancer. His performance then won him the promotion to chief operating officer in 2005.
Analysts credit Cook with solving problems that Apple was having with inventory management. That has been key to Apple's ability to amass $25 billion in cash and short-term investments. Many people consider Cook as Jobs' logical successor.