The top seed pipped Cuevas in a first set tie-break and denied his opponent two set points in the second but succumbed to his first defeat against the world number 45.
“I lost an opportunity, that’s it,” Spaniard Nadal said after being denied his 100th ATP final by claycourt specialist Cuevas who fired 48 winners to clinch the contest.
“I fought until the end. I have to accept it and keep working to try to change the dynamic. That’s what’s happening today and I have to work hard to change it,” added the 14-times grand slam champion.
“I didn’t win a title, so it wasn’t a positive two tournaments. I had my chances in both. I lost in the semi-finals of both tournaments and just have to look forward to Indian Wells.”
Cuevas will meet another unseeded player in Guido Pella in the claycourt final after the Argentine’s 6-1 6-4 humbling of fifth seed Dominic Thiem, who beat Nadal in the semi-finals in Buenos Aires last week.
World number five Nadal, who failed to win a grand slam title last year for the first time since 2004, entered the season positive after an injury-free off-season but was dumped out of the first round of the Australian Open and has struggled to return to his best form since.