Samaniego started his football career in the youth divisions of Club Olimpia of Paraguay.
He played for Olimpia from 1981 to 1985, achieving the top scorer title of the Paraguayan League in 1985 and winning the national championship in 1981, 1982, 1983 and 1985.
After a brief stint in Mexico playing for Necaxa, he returned to Olimpia in 1990 to form the feared attacking trio of 1990 along with Raul Vicente Amarilla and Gabriel "El Loco" González, which led Olimpia to the Copa Libertadores title, Supercopa Sudamericana and Recopa of the same year.
Samaniego made his international debut for the Paraguay national football team on 9 October 1985 in a friendly match against Chile (0-0).
He obtained a total number of 26 international caps, scoring seven goals for the national side.