The match was due to be played on Thursday but they only got as far as the warm-up before one of numerous rain breaks sent them back to the locker room.
Nadal is not used to playing the first match of the day so perhaps the early start explained his lethargy on a cool and blustery Court Suzanne Lenglen.
The Spaniard does not like such conditions, which reduce the effect of his spin, while he also tends to have a tougher time against fellow left-handers.
Nadal said: "In the first set I simply was not motivated enough. I tried, but I couldn't find the necessary motivation.
"Yesterday [Thursday] I just warmed up for half an hour, so I haven't played much tennis for three days. That makes things not easy.
"So I started the match probably with not the right intensity, with more doubts than usual.
"The positive thing was that I had a good reaction at the beginning of the second set. Even if I didn't play fantastic, I played the way that I had to play, with intensity, with passion.
"I'm just happy to be through at the end. That's the real thing. The most important thing is win on these kind of days, and hopefully the conditions will improve, because with these conditions it is not easy to play well."
Nadal certainly played well below the standards that have brought him six titles from eight tournaments this year, making uncharacteristic mistakes and dropping his groundstrokes far too short.
Klizan, ranked 35 in the world, played well but he did not have to produce anything too special to win the first set, breaking Nadal's serve in the seventh game.
Seven-time champion Nadal also lost the first set against Daniel Brands in the opening round, but on that occasion his opponent really came out blazing.
Nadal did not turn things around until the end of the second set on Monday having been 3-0 down in a tie-break, but this time his reaction was immediate as he won four straight games.
The Spaniard was pinning his opponent to the baseline now, and although Klizan pulled one break back, Nadal avoided another wobble.
He was still not playing particularly well but it was good enough to stay ahead of Klizan, who lost to Britain's Dan Evans in Davis Cup last year but also upset Jo-Wilfried Tsonga at the US Open.
Nadal looked in complete control when he moved 5-1 ahead in the decider but Klizan broke again when the Spaniard served for the match.
That was as far as the Slovakian's comeback went, though, and Nadal served it out at the second time of asking to win 4-6 6-3 6-3 6-3.
Next up for the third seed is talented Italian Fabio Fognini, who put out Nadal's Wimbledon conqueror Lukas Rosol in round two.
He said: "I think everybody knows in this room that the schedule of yesterday [Thursday] was wrong. That's the real thing.
"The director of the tournament, supervisors, they take a bad position two days ago, because when you make the schedule at 7pm, you know what weather predictions you have for the next days.
"I cannot play third after a men's and a girl's match when my possible opponent plays second after girls. That's not fair. And today I was playing almost three hours on court, and my opponent was watching the TV in the locker room.
"So if you told me that's fair, I say that's not fair. The only thing that I can do is be positive, smile, and try to win my match and try to be ready for tomorrow [Saturday].
"But that's not the right thing. This is not right. And I hope they accept the mistake.
"The excuse they told me was because Rosol have to play doubles. I am sorry, but that's a joke. You have one more week to play doubles if you want to play doubles.
"Why do you want to protect the player who has to play doubles? So I'm going to write myself in the doubles draw then and I have the priority to play? That's not the right excuse to make a schedule like this."