The two biggest names in golf had been paired together at the Abu Dhabi HSBC Championship but, in a huge blow to the fans with tickets for the weekend action, neither will be around after both shot second-round 75s.
That came after Woods found himself in trouble over an embedded-ball incident on the fifth hole and once off the course had his bogey five turned to a triple bogey.
Instead of being one over and safely in for the closing 36 holes, his score was changed to three over - one stroke too many.
European Tour senior referee Andy McFee, alerted after two journalists spoke to another of the referees, told Woods on the 11th hole that there was an investigation going on, but it was only after the round that the penalty was imposed.
"Andy feels the way he feels about it and I broke the rules," Woods said.
As for McIlroy, unveiled this week as the new mega-million face of Nike, he could not save himself despite changing to an old putter on his return to the course.
"I just felt the greens I have been practising on were much faster. It was just a weight issue," the 23-year-old Northern Irishman said being before asked if his new equipment company were fine about him not using one of their putters.
"I'm not here to talk about my (Nike) contract. I'm here to talk about my golf," he replied. "I've got four weeks to work on it. I knew it was going to be a tough week (his deal was unveiled on Monday). I hit the ball really well in Dubai last week, but it just got worse for some reason."
England's Justin Rose continued to enjoy himself in the desert sun, meanwhile. The 32-year-old currently ranked fifth in the world added a 69 to his opening 67 and on eight under par was one ahead of Welshman Jamie Donaldson, Dane Thorbjorn Olesen and Spaniard Gonzalo Fernandez-Castano.