The body of Hannelore Kohl, 68, was today found at the family's home in the west German city of Ludwigshafen, according to Rhineland-Palatinate state officials.
She had been suffering for seven years from a painful sunlight allergy that virtually kept her a prisoner indoors.
A statement from Mr Kohl's office in Berlin said that the allergy had forced Mrs Kohl to spend the last 15 months of her life at the family's home without any daylight.
"Due to the hopelessness of her health situation, she decided to end her life of her own free will," the statement said.
"She conveyed this decision in farewell letters to her husband, her sons and friends."
The statement said that she was taking strong painkillers, and that doctors in Germany and abroad had failed to alleviate the extremely rare ailment. It is not yet known how she killed herself.
She married Mr Kohl in 1960 and stood firmly by his side throughout his time as German chancellor from 1982 to 1998.
Her coiffed blonde hair and blazers earned her the title of "the Barbie of the Rhineland" from her critics, but she supported her husband throughout the corruption scandal that enveloped him after he was voted out of office.
She has rarely been seen in public since her husband's election defeat in 1998.
Condolences have poured in from Mr Kohl's political friends and foes, including the German chancellor, Gerhard Schröder, who wished Mr Kohl and the couple's two sons "courage and strength to live with this terrible loss".
"Hannelore Kohl will be remembered as a woman who fought for the rights of others," said Mr Schröder. "She gave many people courage."
A few years ago, she authored a cookbook with her husband that extolled the heavy German fare he loves, such as stuffed pig's stomach.
In May, she was so stricken by her ailment that she had to skip the wedding of her son Peter to his Turkish fiancee in Istanbul, Turkey.
Mrs Kohl's allergy was triggered by a penicillin treatment in 1993. She acknowledged it was untreatable, and her condition worsened last year.
In a recent interview with the Süddeutsche Zeitung newspaper, she expressed sadness that the couple's Berlin apartment was too bright for her to spend much time in.
Since being voted out as chancellor, Mr Kohl has split his time between his native Rhine river region and the capital.
Mrs Kohl was born on March 7 1933 in Berlin, the daughter of an engineer. She grew up in the east German city of Leipzig until the end of the second world war in 1945, when the family moved west.
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Süddeutsche Zeitung newspaper
