It came down to a nail-biting decider against English duo Sophie Thornhill and Helen Scott in the final of the women's para-sport sprint B tandem.
Paisley-born McGlynn, 41, displayed the mettle that has made her a triple Paralympic champion as she and her sighted pilot, 33-year-old Haston, from Edinburgh, pushed reigning double world champion Thornhill and Scott to the wire.
The first race was lost by little more than a wheel rim, before the English pair went on to win the second and claim their place on the top step of the podium.
Draped in a saltire, McGlynn and Haston insisted they would go away happy, knowing that they had left everything out there on the track in pursuit of victory. "We were aiming for gold but the competition was really stiff and I'm really pleased with our efforts," said McGlynn. "When the crowd roared, my heart was going like the clappers. We gave it everything."
"It was unbelievable," added Haston. "We have raced here at the Scottish Championships before a handful of people. To race in that jam-packed arena is amazing.
"I'm delighted to come away with a silver medal. I can't wait until Sunday to hear that home crowd cheer us on in the 1000m time trial."
McGlynn, who is registered blind, competed in the 2012 Paralympics in London, taking a silver and bronze. She won gold in Athens in 2004 and was a double champion four years later in Beijing.
"My best achievement is to win my two gold medals in Beijing, but just to race in Scotland with the saltire on my back has made me so proud and I'm enjoying the Games," she said.
Double world silver medallist Brandie O'Connor and Breanna Hargrave, of Australia, took bronze ahead of their compatriots, Paralympic and three-time world champion Felicity Johnson and Holly Takos.
Earlier, a thrilling morning session saw records fall thick and fast. McGlynn and Haston set a new Commonwealth Games record in the flying 200m during qualifying of 11.419sec, before being usurped only moments later by Thornhill and Scott with a time of 11.277sec.
Scots pair Laura Cluxton and Fiona Duncan finished fifth in the women's para-sport sprint B tandem after seeing off the challenge of Rhiannon Henry and Rachel James, of Wales, in the minor placings. It marks a commendable effort for Aberdeen-born Cluxton, who only joined Scottish Cycling's performance programme last November. Both Scots pairs will compete in the women's para-sport 1000m time trial B tandem on Sunday.
In the men's sprint, the Games record for the flying 200m was broken no fewer than four times during qualifying with Australia's Matthew Glaetzer posting the fastest time of 9.779sec.
Callum Skinner was the highest placed among the Scottish contingent. He progressed to the final 12 clocking 10.198sec in qualifying, before losing out to Sam Webster, of New Zealand, in the first round. Fellow Scots John Paul and Chris Pritchard finished 14th and 18th respectively.
Australia's Anna Meares successfully defended the women's 500m time trial title she won in Delhi four years ago, setting a new Games record of 33.435sec. Team-mate Stephanie Morton took silver and England's Jess Varnish the bronze. Scots Eleanor Richardson and Jenny Davis finished eighth and ninth respectively.
Jonny Biggin, Pritchard and Skinner, meanwhile, missed out on a place in the bronze medal race in the men's team sprint to Canada by an agonising 0.19sec. It was New Zealand who proved triumphant with a Games record of 43.181sec with England second and Australia third. Scotland placed fifth overall.
Today's action will see Scotland's Katie Archibald contest the women's 3000m individual pursuit, while Neil Fachie and Craig MacLean get their campaign under way in the men's para-sport 1km time trial B tandem.