The Spaniard who has lost only once in eight years at Roland Garros, was a set and 3-0 down in the second-set tie-break before finally subduing the 59th-ranked Brands.
Playing his first grand slam match since crashing out of last year's Wimbledon to lowly-ranked Czech Lukas Rosol, history threatened to repeat itself as Brands, who had never won a match at Roland Garros in four attempts, dictated the early stages.
Nadal, down to fourth in the rankings after seven months out injured, broke in the first game of both the third and fourth sets to wrestle back control of the match.
"I know he was playing unbelievable tennis," Nadal said in his courtside interview. "I tried to find my game and to resist his fantastic shots. I am very happy to be through in this fantastic game."
"I think he didn't know me until the match, and I think he was surprised," Brands said of his illustrious opponent. "Maybe I was too sure to win the point and lost a little bit concentration on this ball, and normally that shouldn't happen against him.
"Maybe that was the turning point."
Nadal surged on to the court with his usual bouncing gait, but that was where all familiarity with the king of the Parisian clay ended.
Since returning in February, Nadal has won six of his eight tournaments and is on a 15-match winning streak, but he looked heavy-footed as Brands's steeplejack serve and pounding flat forehands blew holes in the Spaniard's defences.
Murmurs of disbelief echoed around a sun-bathed Philippe Chatrier court as Brands pulled off the unthinkable feat of breaking Nadal in the ninth game when the 11-times Grand Slam champion dumped a second serve into the net.
The German wrapped up the set in 36 minutes with one of many huge forehand winners and had Nadal looking listlessly to the skies for inspiration when he failed to convert a breakpoint in the second game of the second set.
The turning-point came in the tie-break, when after conceding the first three points, Nadal won seven of the next eight to level the match.
An immediate break at the start of the third brought back something resembling the natural order and with the German's resolve weakened, Nadal strode clear with two further breaks in the fourth.
Next up for Nadal is a second-round clash with Slovakia's Martin Klizan or American Michael Russel.
Gael Monfils, whose career has recently been hampered by injuries, returned to the French Open with a bang on Monday to beat Czech fifth seed Tomas Berdych in a first-round marathon.
Monfils, the world number 81, prevailed 7-6 6-4 6-7 6-7 7-5 in front of an ecstatic Court Philippe Chatrier crowd after four hours three minutes.
The Frenchman, who reached the semi-finals at Roland Garros in 2008 and missed last year's event because of a knee injury, wrapped up the match with his fourth match point when Berdych sent a backhand long.
He will next face Latvia's Ernests Gulbis.
Another local favourite, Jo-Wilfried Tsonga, barely broke sweat as he brushed aside Slovenian Aljaz Bedene 6-2 6-2 6-3 to book his place in the second round.
The sixth-seeded Tsonga, the last French man to reach a Grand Slam final at the Australian Open in 2008, will next take on either compatriot Paul-Henri Mathieu or Finn Jarkko Nieminen.
Tsonga, who could run into second seed Roger Federer in the quarter-finals, simply had too much power and pace for Bedene, who was playing his only second grand slam match.
The 28-year-old Frenchman ended the contest on Court Suzanne Lenglen on his first match point with a service winner.
Michal Przysiezny (Poland) beat Rhyne Williams (U.S.) 6-3 6-7(5) 7-5 7-5
21-Jerzy Janowicz (Poland) beat Albert Ramos (Spain) 7-6(3) 7-5 6-3
Gael Monfils (France) beat 5-Tomas Berdych (Czech Republic) 7-6(8) 6-4 6-7(3) 6-7(4) 7-5
Albert Montanes (Spain) beat Steve Johnson (U.S.) 6-4 3-6 6-3 3-6 6-1
Jarkko Nieminen (Finland) beat Paul-Henri Mathieu (France) 6-4 4-6 7-6(9) 4-6 6-2
19-John Isner (U.S.) beat Carlos Berlocq (Argentina) 6-3 6-4 6-4
Robin Haase (Netherlands) beat Kenny De Schepper (France) 6-4 7-6(3) 2-6 6-3
Daniel Gimeno-Traver (Spain) beat 17-Juan Monaco (Argentina) 4-6 4-6 7-6(4) 6-4 6-4
Ernests Gulbis (Latvia) beat Rogerio Dutra Silva (Brazil) 6-1 7-6(4) 6-3
7-Richard Gasquet (France) beat Sergiy Stakhovsky (Ukraine) 6-1 6-4 6-3
27-Fabio Fognini (Italy) beat Andreas Beck (Germany) 6-3 7-5 6-3
Martin Klizan (Slovakia) beat Michael Russell (U.S.) 3-6 6-3 6-1 0-0 (Russell retired)
Lukas Rosol (Czech Republic) beat Pere Riba (Spain) 6-3 6-4 6-4
3-Rafa Nadal (Spain) beat Daniel Brands (Germany) 4-6 7-6(4) 6-4 6-3
11-Nicolas Almagro (Spain) beat Andreas Haider-Maurer (Austria) 4-6 6-4 6-3 6-3
30-Julien Benneteau (France) beat Ricardas Berankis (Lithuania) 7-6(5) 6-3 5-7 7-6(5)
10-Marin Cilic (Croatia) beat Philipp Petzschner (Germany) 6-1 6-2 6-3
Pablo Cuevas (Uruguay) beat Adrian Mannarino (France) 6-3 2-6 6-3 5-7 7-5
Tobias Kamke (Germany) beat Paolo Lorenzi (Italy) 6-3 6-3 3-6 0-6 6-3
Grega Zemlja (Slovenia) beat Santiago Giraldo (Colombia) 6-1 6-4 6-1
6-Jo-Wilfried Tsonga (France) beat Aljaz Bedene (Slovenia) 6-2 6-2 6-3
Evgeny Donskoy (Russia) beat Jan-Lennard Struff (Germany) 7-6(7) 2-6 7-6(2) 6-2
Nick Kyrgios (Australia) beat Radek Stepanek (Czech Republic) 7-6(4) 7-6(8) 7-6(11)
Feliciano Lopez (Spain) beat 31-Marcel Granollers (Spain) 7-5 2-6 6-4 4-6 6-4
Edouard Roger-Vasselin (France) beat Martin Alund (Argentina) 6-2 4-6 6-1 6-0
32-Tommy Robredo (Spain) beat Juergen Zopp (Estonia) 6-3 6-2 6-1
Igor Sijsling (Netherlands) beat Jurgen Melzer (Austria) 6-4 6-3 6-2
13-Kei Nishikori (Japan) beat Jesse Levine (Canada) 6-3 6-2 6-0