SmithKlineBeecham says it was meant to harm the launch of its new AIDS treatment, which requires use of Norvir.
The company also contends "Juror B" was removed simply because he was gay.
"It's a big deal," said Vik Amar, University of California, Davis professor.
Before trials, lawyers for both sides are allowed to use several "challenges" each to remove someone from the jury pool without legal justification.
Abbott says it removed "Juror B" for three reasons, none having anything to do with his sexual orientation. Lawyers said they felt the juror's impartiality was compromised because he was the only potential juror who had heard of the SmithKline treatment, that he was also the only prospective juror who had lost a friend to AIDS and that he worked for courts.
The nation's top court has never ruled on sexual orientation and the removal of jurors.
The U.S. Supreme Court in 1986 prohibited lawyers from using their challenges to remove a potential juror from a case because of race. Eight years later, the high court added gender to the prohibition.
The California Supreme Court has barred the removal of gays from jury pools without justification since 2000, but its rulings aren't binding on federal courts.
"The discrimination at issue here is particularly harmful, because it reinforces historical invidious discrimination within the court system and undermines the integrity of the judicial system," Lambda wrote the court.