The Brownlee brothers blamed their injury-hit build-up after failing to make the podium in the triathlon at the Commonwealth Games.
Defending champion Alistair, nursing a calf injury, dropped out of contention at the start of the the run phase eventually trailling in 10th.
Jonny, who also had an interrupted build-up, finished seventh as South Africa’s Henri Schoeman claimed gold with Australia’s Jacob Birtwhistle second and Scotland’s Marc Austin claiming a surprise bronze medal.
Double Olympic champion Alistair led after the transition from bike to run but quickly dropped back down the field.
He said: “About three quarters of it went alright. I knew I was going to struggle on the run and I was downplaying my chances. I’ve only run a handful of times in the last month or so.
“The last few weeks has been making sure the calf is alright to make sure I could get round properly.
“The swim and bike went well and I was just trying to pull that gap out as much as possible to give Jonny the best chance. It was a shame it didn’t work out for him.”
Jonny added: “It was pretty terrible today. I didn’t feel great. I’ve had ups and downs and I was injured in January so I missed a lot of training but I thought I was going to be better than that.
“I dived in and felt pretty weak on the swim and then I’m normally one of the strongest on the bike but I didn’t feel great. Then I started running and thought ‘oh dear, I’m in trouble here.’
“I had a stress response in my femur at the start of January so I didn’t run for five or six weeks. I’m trying to get my injuries out of the way now.”
Scotland’s Austin came 22nd in Glasgow four years ago but felt he could succeed in Australia.
He said: “I was obviously scared to dream about that kind of thing because it’s way beyond what I’ve done before but I knew I was capable of it. I thought, ‘I could beat the Brownlees here’.”
The Brownlees are due to compete in the team event on Saturday.
Jessica Learmonth won England’s first medal of the Commonwealth Games after claiming triathlon silver. (Mike Egerton/PA)
Jessica Learmonth had earlier claimed England’s first medal of the Games when she won silver in the women’s triathlon.
Learmonth surprised herself as she finished behind Bermuda’s Flora Duffy in 57 minutes and 33 seconds at the Southport Broadwater Parklands.
Learmonth said: “I hadn’t thought it was the first (medal for England), that’s pretty cool.
“I had a bit of a dodgy lead-up to this race. I was hoping for a bit of a better run so I’m a little disappointed with that but I can’t be disappointed coming away with a silver.
“I’ve surprised myself. I thought I could do it but it’s been quite quick.”
Learmonth only started the triathlon aged 22 and competed in her first World Series three years ago.
Team-mates Vicky Holland and Sophie Coldwell came fourth and sixth respectively while Wales’ Non Stanford came a disappointing eighth.