That total represents 25% of the $12m (£9.66m) bonus he was awarded for finishing second behind Tiger Woods on last year's PIP list which rewards the golfers who have the biggest positive impact on the PGA Tour.
Golfers can skip one designated event and still collect their full bonus but McIlroy has now missed two of them, which the PGA Tour created to get the top players competing against each other more often amid a threat posed by LIV Golf.
To miss a second designated event without penalty, players need an excused absence, like an injury, or risk losing part of their PIP payout from the previous year.
World number three McIlroy announced his decision to withdraw from the RBC Heritage at Hilton Head Island in South Carolina on the heels of his missed cut at the Masters, which was his sixth PGA Tour start in nine weeks.
