Eight-time winner Nadal, bidding to be the first man to clinch five Roland Garros titles in a row, had been expected to face a severe test from the 20-year-old world number 57.
But Thiem, who trains for big matches by running through forests carrying tree trunks to build stamina, ran out of steam on Philippe Chatrier court despite showing occasional glimpses of potential.
Nadal took his career record in Paris to 61 wins against a single loss and goes on to face either Leonardo Mayer of Argentina or Russia's Teymuraz Gabashvili.
"But he is a future star, 100 percent. His level of ball is very high, he is strong on the forehand and backhand. He has everything to be a big champion."
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Thiem had beaten Australian Open champion Stan Wawrinka in Madrid and gave 27-year-old Nadal plenty to think about in an eight-minute opening game.
But Nadal proceeded to pounce on Thiem's raw inconsistencies which saw the young Austrian break the Spaniard twice only to be broken himself seven times and commit 41 unforced errors.
Ferrer has made the quarter-finals of all of his last nine majors and such was the ease of his fifth win in five against Bolelli that the most challenging part of his day was fielding questions over his grooming.
"I changed my haircut. That's all. But there is nothing superstitious about it," said the Spaniard.
Donald Young, the former world junior number one who has consistently struggled to live up the huge hype surrounding him, made the third round for the first time by beating Spanish 26th seed Feliciano Lopez 6-3, 7-6 (7/1), 6-3.
"Looking at it again, you might do some things different, but I can't do it now. If I had it over to do again, I probably would do a few things different.