McIlroy slumped to back-to-back 75s in his first tournament since signing a mega-million equipment deal with Nike. He ended up only joint 98th in a field of 126.
Birdies at the eighth and ninth, where he chipped-in after nearly going in the water off the tee, hinted at a possible fightback on Friday, but he bogeyed the long 10th and 14th.
On his decision to change putters he said: "I just felt like the greens that I've been practising on are a lot faster than these.
"The Nike putter is great on that, but getting to here it's just a weight issue more than anything else.
"I can feel the head of the one I used today a little bit better, but the change was to no avail.
"I've got a few weeks off now to work at it and try and get my game in decent shape for the US."
McIlroy's next event is the Accenture Match Play in Arizona next month.
It's very disappointing. You really want to get off to a nice start at the start of the season, but I've got to realise that it is only the start of the season.
"I knew it was going to be a tough week with everything going on, but I was just looking forward to getting to the golf course and getting back to what I do and what I'm comfortable with", the Holywood golfer explained.
"It just didn't work out like that. I hit the ball really well last week in practice in Dubai and just sort of gradually got worse this week for some reason.
"But I'm going to spend the weekend here and practise and work at it with Michael (coach Michael Bannon) a little bit."
McIlroy's Nike colleague Tiger Woods also missed the cut because of a two-shot penalty imposed after he finished on Friday.
The two extra shots were added by European Tour chief referee Andy McFee over an incident at the fifth hole.
It dropped him from joint 49th into a tie for 71st, with only the leading 65 and ties surviving.
"Andy feels the way he feels about it, then I broke the rules," said Woods, who now heads back to America for next week's event at Torrey Pines near San Diego.
The 14-major champion has never before in his professional career missed the cut in a non-PGA Tour event.
Playing with McIlroy and Martin Kaymer, Woods had called the German over to inspect his lie in among the ice plants right of the fifth fairway.
"I thought my ball was embedded and he (Kaymer) agreed. Evidently it wasn't," Woods added.
Two reporters spoke to a different referee out on the course and McFee was then alerted.
"I went and had a look," the experienced official said. "The area has loose, creeping vegetation, but it's pure sand underneath and it didn't look likely that the embedded-ball relief applied to Tiger's situation."