Primoz Roglic (Jumbo-Visma) kept the overall leader’s pink jersey after the fifth stage from Frascati to Terracina was neutralised with nine kilometres remaining for safety reasons due to the treacherous conditions.
Roglic leads Simon Yates (Mitchelton-Scott) by an unchanged 35-second margin and Vincenzo Nibali (Bahrain-Merida) by another four.
Fernando Gaviria (UAE Team Emirates) finished second behind the Ackermann rider with Arnaud Demare third for Groupama-FDJ.
Ackermann, making his grand tour debut, also won Sunday’s second stage from Bologna to Fucecchio.
“All the stage was scary, all the descents, you cannot see that much in the peloton because of all the water,” said Ackermann. “It just was lucky that nobody crashed.”
He said it had been effectively a sprint in two parts to the finish after he had to brake in the last 250 metres before winding up again for the final dash for the line.
Dumoulin (Sunweb), feeling the effects of a big crash on Tuesday, had started the stage but abandoned shortly after the start with his focus now on the Tour de France.
“I wanted to finish it. I am not ready to go home yet,” he said. “I didn’t want to be at home in two days’ time and my knee would be less swollen and I would be able to do a ride and feeling sad that I didn’t try and maybe if I’d pushed through and with some painkillers today it could have been possible.
“I would have always asked myself that question and now I ask myself and know the answer.”
Louis Vervake (Sunweb) was caught 23km from the finish after staging a long breakaway.
The sixth runs 238km from Cassino to San Giovanni Rotondo, with a fast opening 190km and no major climbs before ascending through hairpins.