Jamieson, who lost to Murdoch in the same event at last year's Commonwealth Games in Glasgow, finished in 2:12.16 - 0.85 seconds ahead of his fellow Scot.
"I'd love to go sub 2:10," Jamieson told Scottish Swimming's website.
"I've never dipped below that unrested. I'm heading to Vichy next week for the French Open Championships so I'd like to get close to that then."
Having not qualified for this year's World Championships in Russia, which begin next month, Jamieson is working towards next year's Olympics in Rio.
"Rio is absolutely my goal," added the 27-year-old who won Olympic silver at London 2012.
"I want to get into the best shape possible. We hear all the time how great breaststroke is in the UK. But that's the truth. You need a world class time to make the British team and that is what is pushing us all on.
"I still believe I can get up there and compete with the best.
"I'm not going to Kazan. It's the first time I've not been part of the GB set up since 2009 and that's disappointing. It's not been an easy 12 months but I'm starting to enjoy my swimming again now so I'm all about looking forward."
Also at Tollcross International Swimming Centre in Glasgow, University of Stirling quartet Robbie Renwick, Jak Scott, Cameron Brodie and Jordan Hughes broke the British club record for the 4x200m freestyle by winning in 7:22.18.
Michael Jamieson beat Ross Murdoch in the final of the 200m breaststroke at the Scottish Swimming Championships.