The Swiss number two was downed 6-2 6-4 by Nadal in the final of the Madrid Open on Sunday, and has now lost each of his nine matches with the Spaniard since their maiden duel in the 2007 Australian Open.
Wawrinka will return to the world's top 10 when the new rankings are released on Monday, but Fleming says the 28-year-old may not possess the athleticism to make inroads at the very top of the game.
"The two things that the guys who can compete with Rafa do is hit the backhand across court quite early and quite flat, and move and defend so well," said Fleming, a former Wimbledon and US Open men's doubles champion.
"But Wawrinka hits his backhand with a lot of roll and topspin and even if he gets the right angle he cannot hurt Rafa, while he is not the greatest mover either. You can see why he has lost 18 sets in a row against Rafa as it was a bit of a cakewalk."
Nadal took his number of clay-court titles to 40 with his triumph in his homeland and now sits second on the all-time list behind Argentine legend and 1977 French Open champion Guillermo Vilas, who scooped 46.
Sky Sports pundit Barry Cowan believes the Mallorcan's serve was crucial in his taming of Wawrinka and thinks that having rediscovered his strut after a significant period out of action with a knee injury, the 26 year-old could soon top the world rankings again.
"Wawrinka couldn't make any inroads into Rafa's serve - Rafa only lost seven points on serve in the match - but this was the best we have seen from Rafa in the European clay-court season," said Cowan, after witnessing Nadal win his fifth title of 2013.
"His swagger was there and his footwork was working and when that happens it is very difficult to dislodge him; he came into this final at probably seven out of 10 for the clay-court season but it's only [Novak] Djokovic that has looked like he can beat him
"When he raises his level, as he did against Wawrinka, he is only going to gain more confidence - and there is a distinct possibility he could be number one by the end of the year."
Want more clay-court action? Tune into the ATP Rome Masters from 10am on Monday on Sky Sports 1 HD.