Gomez finished in one hour 48 minutes and 26 seconds, 14 seconds ahead of France's Vincent Luis with South African Richard Murray third, 35 seconds further back.
Murray said potholes and uneven manhole covers on part of the newly-asphalted course caused a few hair-raising moments.
"The course was very good but I think there are a few potholes that are quite dangerous," Murray told Reuters.
"There are badly-placed manhole covers. Some of them were four to five centimetres deep and when you are going 50 or 60km an hour over them it is quite scary.
"But other than that the course was amazing. I am happy (to have qualified)."
Those complaints came after a week of worries over the quality of water off the famous Copacabana beach.
The Atlantic is where triathlon, open water swimming and sailing events will take place and independent studies released have shown unacceptable levels of disease-causing viruses.
Few of the elite triathletes complained about dirty water during the weekend races as they focused exclusively on securing a spot in next year's Olympics.
The top three men guaranteed places for their countries, while in the women's race earlier on Sunday, the U.S., Britain and Germany secured spots.
Gwen Jorgensen took her winning streak to an amazing 12 consecutive races when she won the women's elite event.
The 29-year-old American pulled away from Briton Non Stanford on the final running section to win by 19 seconds in 1:58:46.
Vicky Holland of Britain was third in 1:59:27.
(Writing by Andrew Downie, editing by Ed Osmond)
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