Nadal, going for his record seventh French Open title, and Djokovic, trying to become the first man in 43 years to win four straight major titles, played under a light drizzle for much of the match, which also included a 34-minute interruption in the second set.
Not long after they returned after the first delay, the rain started again. Court Philippe-Chatrier kept absorbing more water but the players had to beat the mushy mess of waterlogged clay out of their shoes on virtually every point.
As he was preparing to serve down 2-0 in the fourth set, Nadal took one of the saturated tennis balls and tossed it toward the chair umpire. Nadal, who had lost the previous eight games, won his serve. But on the changeover, play was called and the rain kept coming into the evening.
It means the French Open won't end on a Sunday for the first time since 1973, when Ilie Nastase's victory over Nikki Pilic ended on Tuesday.
The forecast for Paris calls for intermittent rain Monday.
The stoppage killed a huge momentum shift in the match. Djokovic was down two sets and 2-0 in the third, when he turned things around, hanging in for the long rallies that normally favor his opponent.
He started winning those points and Nadal a master of the clay, though maybe not the mud began looking as helpless as Djokovic had over the first two sets, during which he repeatedly gestured up to his guest box, seemingly looking for answers.
Djokovic spiked one racket to the ground a move that brought boos and whistles. Then, after losing to fall behind 4-3 in the second set, he bashed another stick into his bench, putting a big hole in the bottom.
Tournament officials replaced the bench after the first break. Djokovic came out with clean socks and what seemed like a new attitude. After dropping three quick games, he ran off eight in a row, including the first set he's ever won off Nadal at Roland Garros and the first Nadal has dropped during the 2012 tournament.
