However, 127th-ranked Berrer came out firing winners to all corners of the court to pull off his first victory over a top five player.
"These things happen after a long time without being on the road... being in competition. I was playing with more nerves because after a long time away I wanted to win," world number three Nadal told reporters.
"My motivation and my hunger to keep doing things well is still the same."
Although the 34-year-old German achieved the remarkable feat in his final season on tour, he did not get too carried away by the result.
"It's really unbelievable," said Berrer, who until Tuesday had won just four games against the former world number one.
"Losing 1-6 felt like the other matches against him so I had to do something. It's my last season, I'm going for it, I have nothing to lose, I'm enjoying it here so why not.
"It's one of the matches that will stay in my memory but, let's be honest, it was the first match for Rafa after many months of injuries, so we have to be realistic. But for me great."
Nadal had three break points to level the third set at 5-5 but despite jitters from Berrer, who served two double faults trying to close out the win, the German hung on to watch his opponent whip a service return wide on match point.
While 14-times grand slam champion Nadal must turn to plan B to get ready for the season's first major, having produced 32 unforced errors, there were no such problems for Novak Djokovic who polished off fellow Serb Dusan Lajovic 6-2 6-1.
Making his first appearance at the hardcourt event as he cranks up his Australian Open build-up, Djokovic showed no sign of the illness that sidelined him at last week's Abu Dhabi exhibition event as he eased through to the second round.
World number one Djokovic ended last year with back-to-back titles and nothing in a 57-minute demolition of Lajovic suggested he will be any less of a force this year.
Lajovic briefly made a match of it in the opening set but was powerless to stop an eight-game winning streak for ruthless Djokovic who displayed his trademark clinical precision.
The Serbian top seed, who will bid for a fifth Australian Open title this month, next faces Ukraine's Sergiy Stakhovsky.
(Reporting by Pritha Sarkar and Martyn Herman, editing by Ken Ferris)
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