Yingluck was impeached in 2015 and banned from politics for five years for alleged corruption in the rice-purchasing program.
Judge Cheep Chulamon said he had been informed by Ms Yingluck's lawyer that she was unable to attend becase she was suffering from earache.
The judge said the court did not believe the excuse, however, because no official medical verification was provided. The court issued a warrant for her arrest and a new verdict date was set for 27 September.
A BBC report quoted sources close to her party as saying that she made the decision to leave unexpectedly.
"I am very sad to learn that she is not coming here today", said Pu Baitongsod, a 50-year-old office worker holding back tears.
Supporters of Ms Yingluck consider the arrest warrant as a form of harassment that has turned the former prime minister into a fugitive, Mr Sunai said. She also said that security measures would make it impossible to interact face-to-face with supporters.
This insistence was repeated as late as yesterday, when her lawyer Norrawit Larlaeng told reporters Yingluck would definitely be in court. "Will she still say that she didn't get justice?"
Instead, current Prime Minister Prayut Chan-o-cha said he has "assigned officials to check the normal entry and exit routes and find out where she is".
Her bail of 30 million baht (S$1.2 million), posted when the trial began more than two years ago, has been confiscated.
Her brother, Thaksin, left the country shortly before the court handed down his judgement in 2008.
But critics accused him of abusing power and blurring the lines between business and politics, becoming as loathed by the Bangkok royalist elite as he was cherished by the rural poor.
Paralysing protests and court cases have hacked at their governments and finances, while another coup toppled his younger sister Yingluck in 2014.
According to Wolfram Schaffar, political scientist and Thailand expert from the University of Vienna, "It was absolutely a standard program". Yingluck posted a message on her Facebook page urging followers to stay away, saying she anxious about their safety.
Ignoring her plea, thousands of peaceful protesters showed up outside the court holding roses and wearing white gloves with the word "love" on them.
The rice subsidies, promised to farmers during the 2011 election, helped Yingluck's party sweep the vote. The hope was to drive up prices by stockpiling the grain, but other Asian producers filled the void instead, knocking Thailand from its perch as the world's leading rice exporter. For example, Yingluck shied away from dealing with the gnawing problem of lese majeste cases, which perpetuated a huge negative impact on human rights and political debate.
The government confirmed last month that it had temporarily frozen her properties and bank accounts.
However the Supreme Court rules, the junta is likely to lose face, one analyst said.