Tim Cook, Apple’s (AAPL) chief operating officer and heir apparent, got his today.

For taking the reins when Steve Jobs went on medical leave in Jan. 2009 and heading the company with no visible hitches until his master’s return six months later, Cook was awarded a $5 million cash bonus and 75,000 shares of restricted stock, according to Form 8-K filed with the SEC on Friday.

The stock doesn’t vest until 2011 and 2012, but at today’s close of $226.6, it’s worth $16.995 million.

This was Cook’s second stint as Apple’s acting CEO. He ran the shop for a month in 2004 while Jobs recovered from surgery that removed a malignant tumor from his pancreas (see here). By the time Jobs returned to work, Apple’s shares had risen 10.9% to what seems now like an impossibly low $35.86.

The fact is, Cook runs Apple’s day-to-day operations even when Jobs is around, making the supply chains run on time and freeing his CEO up to cut high-level deals, rub shoulders with Hollywood moguls, and figure out where the puck is going, to paraphrase Jobs’ favorite Wayne Gretzky quote, not where it’s been.

Before the latest bonus, Cook was already company’s highest-paid executive, thanks in part to Jobs’ famous $1 a year salary.

In 2009, according to the Associated Press, 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. His stock holdings before the latest grant included 13,741 shares of Apple and 500,000 restricted stock options that have not yet vested.

For more on what Cook brings to Apple, see Adam Lashinsky’s definitive profile, published in the Nov. 10, 2008 issue of Fortune.

See also:

• Audio: Tim Cook talking about Apple
• The last time Tim Cook ran Apple
• The genius behind Steve
• The day Tim Cook calmed the waters
• Handicapping Apple’s back bench

[Follow Philip Elmer-DeWitt on Twitter @philiped]