Gilchrist, a 200m specialist, had been struggling with a cold, but won a tight finish in 1:01.22. Jamieson took second place in 1:01.24 and both qualified for the European Championships in Budapest in August.
"I put this win down to age and experience," said Gilchrist, 26, who trains in Paris with former City of Edinburgh coach Fred Vergnoux. "I felt in a bit of a hole and not so good yesterday, but it's great to qualify for the 100m and still have the 200m to come."
In the women's 200m breaststroke, Scot Hannah Miley had to settle for silver but admitted she only entered the event as a training run for her specialist medleys.
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 European Championship and Commonwealth Games selection in 2:29.66.
Miley started as favourite but she admitted: "I really only use the breaststroke to get ready for the medley. I used to be dreadful at breaststroke when I was little and it's good to get pushed by the other swimmers. I'm not a specialist in this event and it's really a fluke that I've won it in the past."
The Scottish Commonwealth Games trials are the Scottish Championships in Glasgow in June, and Miley continued: "I love the Commonwealths because it is the one time you get to stand up and show you are proud to be Scottish. But I also love being part of the British team, and the European Championships make it a real double international goal later in the year."
Stirling teenager Lucy Ellis confirmed she is 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).
Sixteen-year-old Ellis clocked 55.76 for third place, and outsprinted the better known Scot, Caitlin McClatchey. A GB team regular for the past six years, McClatchey was a slightly disappointing sixth in 56.49.
The men's 100m freestyle semi-final also produced a changing of the Scottish guard. Stirling teenager Jak Scott qualified for the final in eighth place in 50.82, while City of Glasgow's Robbie Renwick, winner of the 400m freestyle on Monday, was tenth in 51.07. David Carry missed out on 51.12.
Louise Pate, the Scottish record-holder, made it through to this evening's final of the 100m butterfly. She clinched the fifth qualifying place in 1:00.80. Her Edinburgh University colleague, Jessica Dickons, also qualified in the final tenth spot in 1:02.03.
In the race of the day, Loughborough's Lizzie Simmonds pulled off a shock by defeating England's world champion, Florida-based Gemma Spofforth, in the final of the 100m backstroke. Her personal best of 59.43 just edged out Spofforth's 59.46.