Thiem, who secured a 6-4 6-3 victory to move through to the semi-finals, was able to exact some form of revenge on Nadal who had beaten the Austrian world no 7 in both the Madrid and Barcelona finals.
Nadal, 30, a former seven-time champion in the Italian capital, is hoping to secure his 10th French Open title when the second major of the year begins later this month.
However, it was the 23-year-old Thiem who raced into a 5-1 lead against the world no 4, only for Nadal to reduce the deficit to 5-4 with a break of serve before Thiem closed the first set out 6-4.