The former Ulster flyhalf had his contract revoked by the Irish Rugby Football Union (IRFU) following the trial in Belfast.
He has been playing for Perpignan in France and is due to reunite at London Irish with former Ulster coach Les Kiss and ex-Ireland coach Declan Kidney.
"We have met with the club to express our concerns. Their recent decision is not consistent with our values and so we have ended our sponsorship," the company, owner of Irish beer brand Guinness, said in a statement.
Guinness have been linked to the club for some 40 years, since before the professional era.London Irish said they were "understandably disappointed" by the decision and regretted the relationship had ended in such a manner.
"The club has always respected the right for everyone to have an opinion, and their right to express that opinion," they said in a statement.
"London Irish has been open and honest with all of its sponsors, including offering to meet Diageo’s senior management in Dublin in May, 2019. This offer was not taken up."
The trial of Jackson and fellow international Stuart Olding received widespread media coverage across both Ireland and Northern Ireland, where rugby is one of the few sports with one national team drawn from both sides of the border.
The pair were accused of raping the woman in Jackson’s home in the early hours of June 28, 2016. Prosecutors told the trial that Olding entered the bedroom while Jackson was raping the woman and joined in.
Under cross-examination, Jackson repeatedly denied he had forced the woman and that she had followed him to his bedroom on two separate occasions for consensual sexual activity.
(Reporting by Alan Baldwin, editing by Ed Osmond)
