The famous right-wing journalist and politician Carlos Lacerda disliked the result and considered that JK's victory was not legitimate because he didn't have >50% (althouth the constitution of 1946 accepted plurality) and because JK won only because the communists voted for him and the communist party was banned in 1947 (yes, he used this argument!).
I recall sometime in the last few months reading about a case where a victorious presidential candidate was disqualified because his margin of victory came from communist votes, but unfortunately I cannot remember where or when this was. Maybe someone here can help.