The stage had long been set for Glasgow's Jamieson to top the podium in his home city, but when he was shaded by compatriot Murdoch in the heats, it looked as though the pair had been cast in the wrong roles.
And so it proved in the final showdown as Dumbarton swimmer Murdoch touched the wall first with a brilliant Games record of two minutes 07.30 seconds.
Jamieson took second and England's Andrew Willis third.
Thrilled Murdoch said: "There's no way that just happened. I can't believe it. That was amazing. It's a dream come true.
"It was a massive personal best for me. I didn't think I could do that if I'm honest. I'm so surprised. I can't believe it's just happened."
He added: "It's my grandad's 70th birthday today so that swim was for him."
Jamieson was clearly disappointed with second place but said: "Ross has been on great form all season.
"He's dropped huge chunks off his best today so he deserved to win.
"I don't prepare to come second all the time. It wasn't good enough tonight."
Earlier, there were tears as Hannah Miley kicked off the swimming with a successful defence of her 400 metres individual medley title.
The home favourite beat England's Aimee Willmott to the wall in a thrilling first final in a Games record time of four minutes 31.76 seconds. Australia's Keryn McMaster took bronze.
It was the perfect way for the event to start in Glasgow and Miley's reaction was a tearful one, mirrored by coach and father Patrick and a number of those in the crowd.
It was a second straight Commonwealth gold in the discipline for Miley, who took her emotional state into her media duties.
"I'm absolutely knackered. I don't need a swim down because I feel quite light-headed at the moment! I've got so much lactic acid building up," she said.
"Oh my God, that was just incredible. I literally couldn't feel my legs for the last 50 so, when I touched the wall, I was hoping and praying that I could go fast."
Miley lost out to Willmott when the pair last met in January and some had fancied a repeat of that. But Miley ultimately had confidence in her methods, even if she did ask herself some searching questions along the way.
"I've had my scalp taken a couple of times and I've had to stop and take stock, ask: 'Is it really working? Am I going in the right direction?' Miley added. "But I totally trust the work that my Dad has done.
"I've also had to really take ownership of my sport, focus on what I needed to improve, research everything from nutrition to land exercises, work in the water. It has just all worked - thankfully."