In a blanket finish, Gilchrist, a 200m specialist, struck gold won in 1min 01.22sec.
Jamieson took the second place in 1:01.24 and both qualified for the European Championships in Budapest in August. England's Richard Webb was third in 1:01.37.
"I put this win down to age and experience," said Gilchrist, who now trains in Paris with former City of Edinburgh coach, Fred Vergnoux. "This was the target when I came here – to qualify for the 100m and be able to double up at the Europeans."
Jamieson is also a former City of Edinburgh swimmer and trained regularly with Gilchrist before moving to Bath this year. The Europeans will be his first major GB international.
In the women's 200m breaststroke, Scottish favourite Hannah Miley had to settle for a silver medal. Winner of the 200m individual medley on Monday, the Garioch 20-year-old clocked 2:30.27 with the gold going to England's Stacey Tadd, who broke her personal best and clinched her European Championship and Commonwealth Games selection in 2:29.66.
Stirling teenager Lucy Ellis, who used to swim for Edinburgh's Dunedin, confirmed her emergence as a name to watch in Commonwealth Games year by taking a bronze medal in the 100m freestyle. England's Fran Halsall, the world championship silver medallist, won in 54.71, just edging out her Loughborough training mate, Amy Smith (54.86).
Ellis, 16, clocked 55.76 for third place, and out-sprinted the better-known Scot, Caitlin McClatchey. A GB team regular for the past six years, McClatchey was a slightly disappointing sixth in 56.49.
Louise Pate, the Scottish record-holder, made it through to this evening's final of the 100m butterfly. She clinched the fifth qualifying place after swimming 1:00.80 in her semi-final. Her Edinburgh University colleague, Jessica Dickons, also qualified in the final tenth spot in 1:02.03.