Bahamian Miller-Uibo, who dramatically dived over the line to win Olympic 400m gold at the 2016 Rio Games, swept into the 200m final in 22.95 seconds, nearly half a second ahead of Thompson, easing up behind her.
It sets up an intriguing final on Thursday when Thompson will attempt to win Jamaica's first non-hurdles sprint title of the Games, following Yohan Blake's shock defeat in the men's 100m.
Thompson's outing came after Aisha Praught had broken Kenya's stranglehold on the women's steeplechase, a result that also gave Jamaica its first Commonwealth medal in a race longer than 800m.
American-born Praught caught Kenyan favourite Celliphine Chespol on the final bend to win in 9min 21sec, ending the East African nation's phenomenal record of sweeping the podium at the last two Games. Chespol took silver and countrywoman Purity Cherotich Kirui bronze.
"I just put in the work every day and believe that I can race anyone," said Praught. "I knew the Commonwealth Games was what I wanted and I worked towards it every day."
Her victory came as Jamaica were urged on by Bolt, who arrived for his first championships as a spectator following his retirement last year.
"I always expect Jamaicans to come out and do their best," said the eight-time Olympic champion. "We are a big track nation so we always expect the best of them at all times."
However, Stephenie McPherson missed the memo as the defending champion was dethroned in the 400m, finishing third behind Botswana's Amantle Montsho, who clocked 50.15 ahead of Jamaica's Anastasia Le-Roy.
Praught's wasn't the only breakthrough performance, as Australia's Kathryn Mitchell unleashed the world's longest javelin throw in five years to win gold with a mighty effort of 68.92m.
"I tried to put all thought of results out of my mind," she said. "I knew I could throw the Australian record eventually, so I just said to myself, 'Allow it to come'."
South African Luvo Manyonga, a former crystal meth addict turned Olympic silver medallist, leapt a Games-record 8.41m to capture long jump gold, while Australia's Brandon Starc won the high jump with a personal best of 2.32m.
Bushy-bearded Daniel Repacholi won his third Commonwealth gold with victory in the 50m air pistol, and India's Shreyasi Singh claimed her first in the women's double trap.
England's Jack Laugher retained his one-metre springboard title but there was heartbreak for Australia's Maddison Keeney and Annabelle Smith, who led the women's 3m synchro until they botched their final dive and finished last.
Malaysia's Lee Chong Wei swept into the last 16 of the men's badminton singles when he dismantled Isle of Man's Benjamin Li in just 21 minutes, dropping only nine points.
India's K Srikanth joined him in the next round — along with formidable Indian women's players Saina Nehwal and PV Sindhu, all three winning with ease.
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