Judge Willem van der Merwe told a packed Johannesburg High Court in a verdict that was broadcast live on national television on Monday: "I find that consensual sex took place between the complainant and the accused."
Zuma's trial has fanned tensions in the ruling African National Congress (ANC) where he remains a popular figure and was until recently seen as the frontrunner to succeed Thabo Mbeki in 2009 as president.
More than 2,000 pro-Zuma supporters staged a noisy demonstration outside the court, the latest in a series of protests attesting to the grassroots popularity of a man many call "JZ".
The 64-year-old anti-apartheid veteran had pleaded not guilty to raping his accuser at his Johannesburg home last November.
But his lawyers said he did have consensual sex with the woman, a 31-year-old Aids activist.
Supporters of Zuma demonstrate
outside the court
Conviction for rape could have brought a jail term of up to 15 years.
Zuma was charged following a separate graft scandal last year which prompted Mbeki to sack him as the country's second-highest official.
He is due to go on trial in July on the corruption charges, which he has denied and described as part of a shadowy political plot by his enemies in the ANC to end his presidential hopes.