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.
Get the best features, fun and footballing frolics straight to your inbox every week.
Thank you for signing up to Four Four Two. You will receive a verification email shortly.
There was a problem. Please refresh the page and try again.