Felicitas Rohrer, is seeking â‚¬200,000 (Â£145,000; $220,000) in damages following the life-threatening illness.
The case is the first of its kind in Germany, Bayer's home country. The firm has already faced a series of law suits in the US and elsewhere.
Bayer insists that its contraceptive pills are safe when taken correctly.
Ms Rohrer, 31, says she would never have taken Yasminelle if the increased risks of blood clots had been made clearer by Bayer.
She launched her lawsuit in 2011 and the civil case opens in the south-western city of Waldshut-Tiengen on Thursday.
In 2009, as a healthy 25-year-old, she collapsed and her heart stopped for 20 minutes.
Doctors found massive clots blocking the main artery to her lung and suggested the contraceptive pill could be to blame.
Ms Rohrer must now take an anti-coagulant, which reduces her chances of conceiving a child. She studied to become a vet but now works as a journalist as she cannot stand for long periods or lift heavy weights.
She accusing Bayer of failing to sufficiently warn women of the increased risks of thrombosis with its Yasmin range of contraceptive pill, which contains the progestin drospirenone.
Bayer rejects the accusations it concealed the dangers as "unjustified", according to AFP news agency.
The company has already paid out some $1.9bn to thousands of women in the US over the alleged side effects.
Source: NHS Choices, MHRA
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Medical notes: Pulmonary embolism
Ms Rohrer is suing Bayer for â‚¬200,000 but told AFP: "The money cannot compensate for what I and other women have gone through."
She said: "What I really hope for is justice," adding that she hoped to see Yasminelle withdrawn from the market.
In 2013, France temporarily banned the sale of Bayer's Diane-35, an oral acne treatment often used as birth control, after four deaths were linked to its use.
Bayer is also the target of a growing number of lawsuits in the US over the contraceptive implant Essure, which women complain has caused them pain and severe bleeding.
A German woman is suing pharmaceuticals giant Bayer, claiming its contraceptive pill Yasminelle caused her to suffer a pulmonary embolism.