The towering frontman scored standout efforts either side of half time to cancel out a leveller from Pepe, as Oscar Tabarez's charges turned in a memorable defensive showing to reach the last eight of the showpiece tournament.
Uruguay started proceedings with plenty of energy as Portugal found themselves up against an industrious press from the South Americans on the shores of the Black Sea.
It took just seven minutes for Tabarez's men to find an opener as Edinson Cavani produced a goal worthy of the world stage.
The Paris Saint-Germain forward started the move as he dropped deep to switch the ball across the pitch for Luis Suarez, who turned inside on his right to swing a ball towards the back post, where Cavani rose to flash a header past a stranded Rui Patricio.
For all of Portugal's endeavour for an equaliser, Uruguay showed standout organisation to silence the Iberians and they almost doubled their lead, Suarez forcing a smart reaction save from Patricio, who dived late to palm away the forward's free kick from the bottom corner.
Portugal continued to press for parity throughout the first half, but Tabarez's men defended with commendable application and adroit coordination, with both Diego Godin and Jose Gimenez producing standout performances at the back.
The Iberians moved the ball quicker after the break and they were rewarded with an equaliser in the 55th minute. For the first time in the game Uruguay fell asleep at the back just as Raphael Guerreiro collected a short corner and delivered into the box, leaving Pepe to break free of his marker and power a header beyond Fernando Muslera.
Parity was to last just seven minutes, however, as Cavani soon returned to haunt the Portuguese defence with his second of the night in the 62nd minute.
Nahitan Nandez took hold of the ball on the edge of the box before slipping in a perfectly-weighted pass for the frontman, who opened up his body to send a memorable, curling finish with his first touch beyond Patricio and into the far corner.
Uruguayan mishaps were rare at the back although keeper Muslera almost gifted Portugal another leveller when he rushed off his line only to spill the loose ball into the path of Bernardo Silva, who could only drive an effort over the bar with the stopper stranded.
Ronaldo and company continued to bang on the door as the game moved into its dying embers, but Uruguay held firm to cap off a remarkable defensive showing in order to seal victory and move into the last eight, where Didier Deschamps and Les Bleus await.
URUGUAY (4-4-2): Muslera; Caceres, Gimenez, Godin, Laxalt; Torreira, Nandez (Sanchez 81'), Vecino, Bentancur (Rodriguez 63'); Suarez, Cavani (Stuani 74')
PORTUGAL (4-4-2): Patricio; Ricardo, Fonte, Pepe, Raphael; Mario (Fernandes 84'), Bernardo, William, Adrian (Quaresma 65'); Guedes (A. Silva 74'), Ronaldo