Woods, 46, beat the world number one to top spot on the PGA Tour’s ‘Player Impact Programme’ (PIP).
The scheme was introduced last year to reward competitors for generating positive interest in the PGA Tour.
McIlroy, who earned $18m (£15m) when he won the Tour’s 2022 FedEx Cup title, got $9m (£7.5m) for being second.
Woods also won the inaugural bonus programme in 2021.
The PIP was designed to reward players who generate the most interest in the PGA Tour, with metrics such as Google searches, news article mentions and social media reach and engagement taken into account.
As in 2021, Woods played a limited schedule this year even before his last tournament in Scotland in July as he continues to recover from injuries sustained in a car crash in February last year.
This season, the 15-time major winner finished 47th at the Masters, withdrew from the US PGA Championship after three rounds and missed the cut at the Open Championship.
McIlroy’s $12m reward arrived just two days after the 33-year-old captured the DP World Tour’s order of merit title for the fourth time.
The Northern Irishman became just the second player to win the FedEx Cup and Race to Dubai titles in the same season after Henrik Stenson in 2013.
Three-time major winner Jordan Spieth won $9m (£7.5m) for finishing third in the PIP, ahead of fellow American Justin Thomas and Spain’s Jon Rahm.
England’s Matt Fitzpatrick, who won the US Open in June, earned $5m (£4m) for finishing inside the top 10 while Ireland’s Shane Lowry picked up $3m (£2.5m).
Last year’s PIP runner-up Phil Mickelson was ineligible after leaving the PGA Tour to play on the Saudi Arabian-backed LIV Tour.
Bryson DeChambeau, Dustin Johnson, Brooks Koepka and Bubba Watson, who were all in the top 10 in the inaugural PIP rankings last year, also exited the PGA Tour for LIV.
Woods will return to action in the Hero World Challenge, an event he hosts in the Bahamas, between 1-4 December.
The 82-time PGA Tour winner will also partner McIlroy against Spieth and Thomas in The Match, a 12-hole exhibition in Florida, on 10 December.