The forward was ruthless in front of goal as Paulo Bento's side capitulated following the dismissal of Pepe in the first half
Paulo Bento's side's chances of getting out of a tough Group G were placed in serious jeopardy as a Thomas Muller-inspired Germany put them to the sword in Salvador on Monday.
Muller - golden boot winner at the 2010 World Cup - continued his superb run at football's showpiece with a hat-trick, taking him to eight goals in seven appearances at the event.
On his 50th Germany appearance, the Bayern Munich man fired his side in front from the penalty spot before Mats Hummels doubled their advantage with a towering 32nd-minute header.
Pepe then tangled with the forward and headbutted him as he sat on the floor, before their woes were compounded by Muller's second on the stroke of half-time.
If Bento thought things could not get worse for his side, he was wrong, as defender Fabio Coentrao was taken off on a stretcher with a suspected groin injury in the second half.
And Muller sealed Germany's big win, capitalising on a Rui Patricio error to tap in with 12 minutes left.
And while the result was a serious statement of intent from Germany - who saw defender Hummels limp off with a late knee injury - Portugal were inexplicably bad, leaving them with an uphill battle to reach the last 16 with games against the USA and Ghana still to come.
Portugal's preparation was largely focused on Ronaldo, who has been plagued by thigh and knee problems in recent months, but he quickly proved his fitness with a sprint and strike at Germany goalkeeper Neuer after Miguel Veloso stripped Philipp Lahm of the ball.
Neuer's opposite number, Patricio, then gave Sami Khedira an excellent chance to open the scoring when he scuffed a horrendous clearance, but the midfielder saw his 40-yard snapshot curl agonisingly wide with the goalkeeper beaten.
Germany did not have to wait long to take the lead though, as Mario Gotze wriggled past Joao Pereira and was hauled down, allowing Muller to fire the resulting spot-kick into the bottom-left corner in the 12th minute.
Almeida limped off just before the half-hour mark, replaced by Eder, and they were soon two down when Hummels rose above Pepe and Bruno Alves to power a header past Patricio from Toni Kroos' outswinging corner.
There were still fleeting moments for Portugal fans to get excited about, as Nani broke well but missed Ronaldo with a pass, before Coentrao, perhaps surprised at finding himself on side, crossed for the talisman instead of shooting in a good position.
But Portugal's hopes quickly unravelled after Pepe's moment of madness.
The centre-back put a hand in the face of Muller as the pair both battled for the ball and the German appeared to make the most of the contact.
But Pepe's decision to push his head into a sitting Muller left referee Milorad Mazic with no choice but to send him off.
And there was still time for Germany to score again as Muller capped a truly miserable half for Bento's men.
Alves' attempted clearance hit Muller in second-half stoppage time, and the ball fell kindly for the forward, who pounced with a predatory left-foot finish that hit Patricio and went in.
Muller nodded over in the second half after an Ozil effort was saved, while at the other end Portugal's plight was summed up when Nani and Coentrao ran into each other inside Germany's penalty area.
Muller then wrapped up the victory, finding himself in the right place to tap in after Patricio spilled a routine cross from substitute Andre Schurrle to seal his treble.