A wave of lawsuits has put pressure on Bayer since its $63-billion takeover of Monsanto a year ago, spooking investors who worry damages payouts could quickly mount into the billions if the firm fails to convince courts its product is safe.
Tuesday's unanimous jury decision in San Francisco federal court was not a finding of Bayer's liability for the cancer of plaintiff Edwin Hardeman.
Hardeman's lawyers, Aimee Wagstaff and Jennifer Moore, said they look forward to presenting that evidence to the jury to hold Monsanto accountable.
The latest case has so far brought no damages award against Bayer, as jurors now have to decide whether Monsanto is liable for the harm suffered by Hardeman.
Monsanto was initially ordered to pay $289m to Johnson, who has two young sons and in the end stages of his cancer, before the damages were reduced to $78.5m.
Regulatory authorities around the world consider glyphosate-based herbicides as safe when used as directed. "And for Mr. Hardeman to have his day in court and to show that Roundup does cause cancer".
Bayer, which acquired Monsanto previous year, said in a statement after the verdict that it continues to "believe firmly that the science confirms glyphosate-based herbicides do not cause cancer".
The trial could pave the way for more cases linking glyphosate in Roundup to the development of cancer.
Shares in Bayer fell more than down 12pc in Frankfurt on Wednesday following the ruling.
"We are confident the evidence in phase two will show that Monsanto's conduct has been appropriate and the company should not be liable for Mr. Hardeman's cancer", Bayer added.
"We continue to believe firmly that the science confirms that glyphosate-based herbicides do not cause cancer", said an online statement from Bayer.
Under Chhabria's order, the second phase would only take place if the jury found Roundup to be a substantial factor in causing Hardeman's non-Hodgkin's lymphoma.
In August 2018 a court suspended licenses for products containing glyphosate, which is widely used in Latin America's agricultural powerhouse, but a higher court lifted the ban the following month.
In the second phase of the case, which starts Wednesday and will determine liability and damages, Monsanto's efforts at influencing public opinion may weigh more than the lack of scientific proof, said Gunther Zechmann, an analyst at Sanford C. Bernstein.
FILE PHOTO: Logo of Bayer AG is pictured at the annual results news conference of the German drugmaker in Leverkusen, Germany February 27, 2019.
However, the Environmental Protection Agency released an assessment in 2017 that concluded that glyphosate is not carcinogenic.
According to European Union health authorities, "experts, with only one exception, concluded that glyphosate is unlikely to pose a carcinogenic hazard to humans and the evidence does not support classification with regard to its carcinogenic potential". It's set to appear in six more trials in federal and state courts this year.