Nadal was competing at his first tournament since Wimbledon, after suffering a right wrist injury.
The world number three was leading by a break in the third set against Klizan, before the Slovakian qualifier exploded - winning 16 of the final 18 points of the match to run out a 6-7 (7-9) 6-4 6-3 victor.
The 14-time major winner said he anticipated a tricky run-in to the 2014 season, after sitting out three months.
"I knew for me it's probably going to be hard, this last part of the season," the Spaniard said.
"It will not be easy after what happened. Always when you are outside for a few months, as I said the other day, it is not the same as if you are coming back the next season and everybody starts from zero.
"You are coming back now, and the other players are on the road, are in rhythm. Physically you feel more tired.
"But on the other side I did well in the past after an injury… I am positive that I can be ready soon and be ready to compete well against everybody soon."
Nadal addressed his durability, claiming he was aware of his limitations but also that he wants to maximise his time in the game.
The Mallorcan also said he is keen to get to the end of the season, and re-charge for the Australian swing in 2015.
"I'm going to work hard with the right attitude to play better than what I did today. I'm going to try," he said.
"I will be happy if I finish the season, take one week and a half holidays, and to practice one month with perfect conditions to try to start the next season with positive feelings.
"I am not 20 years old. I am 28 and a half already, and I need to take care about the things that I am doing because the most important thing for me is be competitive as long as possible."
Nadal is scheduled to appear at the Shanghai and Paris Masters, before the season-ending ATP World Tour Finals in London in November.