Television pictures showed Wu Shu-chen, 54, being carried out of the court by an unidentified woman and loaded into an ambulance waiting outside the courthouse in downtown Taipei.
As she was placed in the ambulance, her eyes were closed and she did not appear to be moving.
A doctor at the hospital where she was being treated said Wu was suffering from an irregularly low temperature and slow heartbeat but there was no danger to her life.
"We gave her some medicine, and her situation improved," said Lin Ho-hsiung of the National Taiwan University Hospital. "She is now under close observation. Her temperature and heartbeat are stable again."
Wu's husband, President Chen Shui-bian, arrived at the hospital shortly after noon (0400GMT) to be with his wife.
Wu's trial began in the shadow of her precarious physical condition, and doubts about her ability to hold up in the face of an expected firestorm of media attention.
She was paralyzed from the waist down when a truck ran her over in 1985, just as Chen and his allies from the nascent Democratic Progressive Party were struggling to break the monopoly grip on power of Taiwan's once dominant Nationalists.
Chen called the incident an assassination attempt and blamed the Nationalists for carrying it out - a charge they deny.
In recent months Wu has appeared frail and sickly, with some reports placing her weight at less than 30 kilograms (66 pounds).
Shortly after the trial began Wu pleaded not guilty to the charges against her.
She was indicted on Nov. 3 with three former presidential aides on charges of skimming 14.8 million New Taiwan dollars (US$450,000; EUR 350,000) from a special presidential fund used to sustain Taiwanese diplomatic activities abroad.
The aides - Chen Cheng-hui, Lin Teh-hsun, Ma Yung-cheng - also pleaded not guilty.
At the time of Wu's indictment, prosecutors said Chen could face the same charges when his immunity lapses after he leaves office.
Chen has said he and his wife are innocent and has promised to step down if she is found guilty.
Wu arrived at the courthouse near the Presidential Office building in downtown Taipei shortly after 9:30 AM (0130 GMT) and was seen chatting with aides.
Seated in her wheelchair, she was lowered electronically from her specially equipped van and wheeled past security officials toward the courtroom.
Her attendance at the proceedings had been in doubt until the last minute because of concerns over her health.
Her trial began amid declining public support for the physician's daughter from southern Taiwan, who was once widely respected for the considerable suffering she endured.
Sympathy for her began to recede in 2005 and early 2006 when it was alleged she had used insider information to make large amounts of money on the stock market, and had been given expensive gift vouchers from an upscale Taipei department store in exchange for helping to arrange for a change in its ownership.
Prosecutors later found there was insufficient evidence to charge her in connection with receipt of the vouchers, but the public outcry following disclosures of her stock trading activities led her to promise to suspend them.
Wu has also been pilloried in the Taiwanese media over her collection of upmarket jewelry, which includes an expensive Breguet watch and NT$6 million (US$185,000; EUR 140,000) jade earrings.
Foes and even some former friends have likened her to the Dowager Empress, the early 20th century Chinese monarch widely reviled for a luxurious lifestyle and willful political maneuvering.
Her indictment has followed nearly a year of nonstop allegations by opposition lawmakers that Chen's family and inner circle exploited their proximity to him for personal financial gain.
On Wednesday a Taipei judge sentenced former Chen aide Chen Che-nan to 12 years in prison for accepting bribes from a businessman to help him solve legal problems.
The two Chens are not related.
Later this month a court in the capital is scheduled to issue a verdict on an insider trading scandal allegedly involving Chen's son-in-law.