The Spaniard, who split the brothers to finish second in London four years ago and has won the world title for the last three years, fractured his elbow in training.
Gomez wrote on Instagram: “I’m really sorry to let you all know that yesterday, when I was just about to finish my bike training, I had one of those silly crashes, no faster than 15 kilometres per hour. Immediately I felt pain in my elbow so we went to the hospital. Scans have confirmed a displaced fracture in the radial head of my left arm. Going into surgery today to fix it.
“Unfortunately this has forced me to pull out of competing in Rio. I need to be realistic, there is no time to prepare and to be fit on the start-line of the Games. The most sensible thing is to vacate my spot and allow someone else the chance to race.
“As you can imagine, this is a really tough time, it’s a goal I have been working for over many years. I’m not done yet. Thanks for the ongoing support.”
Both Brownlee brothers have had a difficult time with injury over the past 18 months but have hit form again, with reigning Olympic champion Alistair winning the last two World Triathlon Series races in Leeds and Stockholm ahead of Jonny.
The men’s race in Rio takes place at Copacabana on August 18.