The jury awarded punitive damages after it found that the St. Louis-based agribusiness had purposely ignored warnings and evidence that its popular Roundup product causes cancer, including Johnson's lymphoma.
Punitive damages are designed to punish companies that juries determine have purposely misbehaved and to deter others from operating similarly.
In a tentative ruling on Oct. 11, Bolanos said it appeared the jurors overreached with their punitive damages award. She said then that she was considering wiping out the $250 million judgment after finding no compelling evidence presented at trial that Monsanto employees ignored evidence that the weed killer caused cancer.
The judge reversed course Monday and said she was compelled to honor the jurors' conclusions after they listened to expert witnesses for both sides debate the merits of Johnson's claim.
The judge said jurors are entitled to accept the conclusion of Johnson's expert witness who said Roundup caused his cancer and reject the conclusions of Monsanto's expert witnesses, who concluded there's no proof the weed killer causes cancer.
"Thus, the jury could conclude that Monsanto acted with malice by consciously disregarding a probable safety risk," Bolanos wrote in her ruling.
Some jurors were so upset by the prospect of having their verdict thrown out that they wrote to Bolanos, the San Francisco Chronicle reported.
"I urge you to respect and honor our verdict and the six weeks of our lives that we dedicated to this trial," juror Gary Kitahata wrote. Juror Robert Howard said the jury paid "studious attention" to the evidence and any decision to overturn its verdict would shake his confidence in the judicial system.
The judge did slash the $250 million punitive damage to $39 million, the same amount the jury awarded Johnson for other damages.
Johnson's lawsuit is among hundreds alleging Roundup caused cancer, but it was the first one to go to trial.
Johnson sprayed Roundup and a similar product, Ranger Pro, at his job as a pest control manager at a San Francisco Bay Area school district, according to his attorneys. He was diagnosed with non-Hodgkin's lymphoma in 2014 at age 42.