The Spaniard was able to move into to the semi-finals without hitting a ball after Dolgopolov succumbed to a shoulder injury in the Brazilian city.
Nadal, who won the event in 2014, will now meet Uruguayan Pablo Cuevas in the final four at the ATP 500 tournament.
Cuevas defeated Argentina's Federico Delbonis 6-4 7-6 (7-4) after the quarter-final clash was delayed for two-and-a-half hours as rain wreaked havoc again.
Play was halted in the second set, with Delbonis leading 4-2 before Cuevas rallied to win through.
Defending champion and second seed David Ferrer, meanwhile, was ousted by Dominic Thiem in the day's final match.
Ferrer's title defence came to an end as the Belgian fifth seed triumphed 6-3 6-2 in an hour, 13 minutes on the clay courts.
In-form Thiem and Guido Pella will face-off in the semi-finals after the latter outlasted Daniel Gimeno-Traver 5-7 6-1 7-5.