Brazilian defender Claudemir gave Nacional an early lead with an eighth-minute penalty at Estadio Dom Afonso Henriques.
The hosts responded well, though, and levelled just after the half-hour mark courtesy of Tomane's fourth league goal of the season.
However, Rondon had the final say, as he struck with just three minutes remaining to earn a valuable three points for the visitors.
The result lifts Nacional above Vitoria and Estoril into fourth place in the Primeira Liga, some eight points adrift of third-placed Porto.
Manuel Machado's side are now unbeaten in their last nine top-flight outings, while the defeat represents Vitoria's second loss in their last three.
