McIlroy admitted to feeling lethargic after shooting a 3-over 73.
Colomo, ranked 506th, recorded a career-best 64 in overcast and windy conditions on the suburban Fanling course.
That earned him a one-stroke lead over fellow Spaniard Miguel Angel Jimenez and Australia's Andrew Dodt.
The 48-year-old Jimenez would break his own record as oldest Hong Kong champion from 2008, and oldest ever winner on the European Tour if he were to capture the title a third time this weekend.
"I am like a good bottle of rioja because I just get better and better with age," Jimenez said with a smile.
Countryman Jose Maria Olazabal put himself in position to end a seven-year winless drought on the tour, playing alongside Jimenez and being among five players signing for 67s.
Olazabal also won in Hong Kong, in 2002.
McIlroy bogeyed his first hole and made his only birdie at the par-5 third hole. He dropped a shot at the sixth after being forced to play his second shot left-handed from beside a bush, and bogeyed 14 and 15.
"I just lacked a bit of energy out there, I felt a bit lethargic and mentally more than physically, if I am being honest," he said.
"I bogeyed the first, but then just got more frustrated as the round went on. I just felt like I was hitting some decent shots and just not really converting any chances for birdies and I just let it go a little bit."
McIlroy believes he's just going through a comedown after securing the tour money title last weekend in Singapore.
"I suppose after last week, and winning the Race to Dubai title, it was always going to be a bit of a letdown," he said. "I feel as though I am playing well enough, but I just need to get my head and the golf to match up and I'll be OK."
Colomo found everything in synch in his Hong Kong Open debut.
He began his round on the back nine and after 10 straight pars he stormed to the top of the board with six birdies over his closing eight holes.
Colomo lost his card last year on Europe's secondary Challenge Tour and this season has been competing on the Asian Tour.
"After losing my card on the Challenge Tour, I was lucky to qualify for the Asian Tour and I'm 33rd on the rankings," Colomo said. "That's perfect, because I now get to play co-sanctioned tournaments like this on the European Tour.
"So it's been a good chance for me to improve, and why not try and win a tournament and get myself onto the European Tour."