A cagey first half offered very little in terms of chances, with the only notable opportunity falling the way of Uruguay, but after evading the Portugal defence, Rodrigo Bentancur was thwarted by the quick reactions of Diogo Costa.
Portugal managed to up the ante in the second period, and their dominance in terms of possession was rewarded with an opening goal in the 54th minute when a dangerous Fernandes cross found its way into the far corner despite Cristiano Ronaldo claiming he got a slight touch.
The Selecao made sure of the three points when they awarded a controversial penalty in stoppage time after the referee Alireza Faghani consulted with VAR and penalised Jose Maria Gimenez for a handball.
Fernandes assumed the responsibility and made no mistake in sending Sergio Rochet the wrong way to secure Portugal's place in the last 16 with a game to spare.
The opening five minutes of the contest suggested an exciting half of football was in store as both sides experienced glimpses of goal.
Mathias Oliviera tried his luck with an ambitious but wayward effort, while at the end of the pitch, William Carvalho sent the ball soaring over the crossbar with a wild right-footed volley.
After an encouraging start to the contest, Portugal dominated possession in a cagey first half where further chances proved to be few and far between, although the best chance of the opening 45 fell to Uruguay's Bentancur.
The Tottenham Hotspur midfielder drove with the intent from the halfway line, before utilising neat and nimble footwork to escape the challenges of the Portuguese defence, but he was unable to find a way past the onrushing Costa.
Portugal began the second period with real attacking intent as Joao Felix went close in the 50th minute, driving a left-footed effort into the side netting.
Four minutes after Felix's miss, Portugal took a deserved lead when initial viewing suggested Ronaldo had produced the deftest of headers from Fernandes's menacing delivery, but on further reflection, the cross found the far corner without any assistance.
After seeing their run of five consecutive World Cup group stage clean sheets come to an end, Uruguay boss Diego Alonso rung the changes in a bid to find a crucial equaliser.
Two of the substitutes both offered an immediate threat, as Maxi Gomez produced a sublime curling strike from the edge of the box, which thundered against the post, before Luis Suarez guided the ball just wide from a promising close-range chance.
In the 79th minute, it was the turn of Giorgian de Arrascaeta to try to restore parity, but he was met by the imposing Portuguese goalkeeper, who made a fine stop to preserve the narrow lead.
Uruguay's hopes of salvaging a point from the contest were quashed in the closing moments, when VAR intervened after Gimenez unintentionally handled the ball as he fell backwards, and following a moment of consultation with the technology, the referee felt Gimenez's infringement was worthy of a spot-kick.
Fernandes showed no signs of pressure as he remained calm and composed to send Rochet the wrong way and roll the ball into the opposing corner.
With a place in the last 16 secured, Portugal will turn their attention to Friday's final group game against South Korea, while Uruguay have to beat Ghana to stand any chance of reaching the knockout stages.