The Spaniard was in deep trouble when the heavens opened – a break down at 3-2 in the final set – but he settled quicker after the restart to win four games in succession.
"My first victory here in 2005 was one of the most beautiful victories of my career," Nadal said after reclaiming the trophy he last won in 2013. "To have this trophy again with me after so many years is really very special."
Nadal was in cruise control after ripping through the opening set in 32 minutes, but a combination of errors and a rejuvenated opponent saw Zverev fight back to level and sneak in front in the decider.
While the 31-year-old has staged countless comebacks in his career, few have been gifted to him quite like the Italian capital’s offering as the elements intervened to rob Zverev of his momentum.
After a 50-minute stoppage, Nadal duly broke immediately and was rarely troubled as he clinched another clay-court title, pinching the world number one ranking back off Roger Federer in the process.
He heads to the French Open as overwhelming favourite to win an 11th title at Roland Garros, while Zverev – who saw his 13-match winning run ended – will hope to improve his dismal Grand Slam record, with the German yet to progress beyond the fourth round.
"You're the greatest clay court player of all time and I think everybody saw that today," Zverev said.