A Rosol double fault allowed former world number one Nadal to take the second set and the decider looked like being a no-contest as Rosol's challenge began to unravel.
Nadal moved a break ahead but, at 4-2, Rosol played some stunning groundstrokes to earn three break points and though Nadal saved two of them he then blazed a forehand long.
There has been no love lost between the players since Rosol stunned Nadal in the Wimbledon second round in 2012, with Nadal gaining revenge at the 2014 Wimbledon tournament.
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Angry looks were exchanged as the decider moved into a tiebreak in which the Spaniard trailed 3-0 before Rosol's forehand deserted him and Nadal won seven of the next eight points to get the job done.
"It was a very tough match emotionally," Nadal, who lost the opening set in 23 minutes, said.
"At the same time, it's a great victory. It's important for me to have these kinds of comebacks. I've been in these situations more times than I would like this year, so I'm happy to win a match like this."
Fourteen-times grand slam champion Nadal, who has already booked his place at the ATP World Tour Finals despite a relatively lean year, will play Bulgaria's Grigor Dimitrov or Ukraine's Sergiy Stakhovsky in round two.
Top seed and local favourite Roger Federer begins his quest for a seventh Basel title on Tuesday against Mikhail Kukushkin.
(Reporting by Martyn Herman; Editing by Frank Pingue/Mark Lamport-Stokes)
