Gomez finished the first two rounds at the 2009 Nationwide Tour opener at 5-under 135.
Henrik Bjornstad (67), Skip Kendall (69) and 2005 champion Vance Veazey (69) are tied for second place at 4-under 136.
Jeff Gove (68), Garrett Osborn (69), Camilo Benedetti (69), Kevin Johnson (70) and Jim Herman (70) share fifth place at 3-under 137.
Gomez made three birdies on the front nine and was suddenly six-under par ' no small feat considering how tough it has been to gain strokes this week at Panama Golf Club.
But then his round took an apparently disastrous turn.
He stumbled to a bogey at the par-4 10th, then made a triple bogey-7 at the 11th after hitting his tee shot into the water. Gomez chalked it up to a loss of concentration.
'I was playing really well and then we got some rain showers to start the back nine,' he said through a translator. 'It affected my concentration and got me in a spin. I got myself squared away and refocused on what I needed to do.'
Gomez, playing in the second-to-last group, was able to overcome his missteps, collecting birdies at the 13th, 15th and 17th holes to take the second-round lead.
The 41-year-old Argentine, who has never won on the Nationwide Tour, picked up a significant title on the Canadian Tour in November when he won the Sport Frances Open by a stroke.
'I came here trying to win this tournament,' said Gomez. 'I don't know if I will, but I have prepared for this particular week.'
Following two days of tough scoring conditions, the cut line fell at 3-over 143. Among those who missed the weekend were the last two champions, Scott Dunlap and Miguel Angel Carballo.