Needing only the Green Jacket to complete a set of all four major titles, McIlroy's fate was pretty much sealed on Friday when he signed for a second round five-over 77 to leave him at five-over for the tournament.
One of the pre-tournament favourites, McIlroy's disappointment dragged on into Saturday as 39 players returned to complete their weather hit rounds where the cut line was set at three over.
The world number two used a late surge to finish runner-up at last year's Masters but has now missed the cut in two of his last three visits to Augusta National.
He is a four-time major champion but it is nearly nine years since his win at the 2014 Open left him needing only a Masters victory to join Gene Sarazen, Ben Hogan, Jack Nicklaus, Gary Player and Tiger Woods as the only players to achieve the career Grand Slam.
One of the PGA Tour's most vocal supporters in their feud with LIV Golf, McIlroy was joined at the exit by six members of the breakaway circuit.
Major winners Bryson DeChambeau (29), Sergio Garcia (43) and Bubba Watson (44) all missed the cut. Kevin Na and Louis Oosthuizen withdrew due to illness and injury respectively.
Ten members of the Saudi-backed series did reach the weekend led by Brooks Koepka (32), who sits two shots clear atop the leaderboard heading into the third round.
Tiger Woods (47) made the cut but by the skin of his teeth when good friend Justin Thomas (29) bogeyed the 17th moving the cut line to three over.
Five-time champion Woods, walking the hilly course on his rebuilt leg, bogeyed the closing hole and finished right on the cut line, tying Gary Player and Fred Couples for most consecutive cuts made at the Masters (23).
"I've always loved this golf course, and I love playing this event," said Woods at the end of his round before the cut line had been set. "I wish I get a chance to play two more rounds."
Couples also became the oldest player in Masters history to make the cut when the 63-year-old returned a second round two-over 74 for a one-over total.
