It was a stunning return to form from the Argentinian, who had scored just once from open play prior to this remarkable blitz against the Magpies at the Etihad Stadium.
Kevin de Bruyne also got on the scoresheet as City, after falling behind to an Aleksandar Mitrovic header during a laboured first-half display, powered back to the top of the table.
Aguero had gone into the game with question marks over his form after a recent knee injury and a patchy display against Borussia Monchengladbach in midweek.
But his late penalty winner in Germany clearly had a rejuvenating effect and for a sparkling period either side of half-time he was world class and unstoppable.
City were ragged and defended badly in the first half but their awakening after the break transformed the game and shredded all of Newcastle's positive early work.
The visitors took the game to City in the first half, although they did have a let-off when Tim Krul palmed away a De Bruyne free-kick and Fernando twice failed to bundle the ball in.
City looked vulnerable out wide and Newcastle's 18th-minute opener came as they cut the hosts open down the left
Chancel Mbemba's initial cross was half-cleared by Eliaquim Mangala but Georginio Wijnaldum quickly returned the ball and Mitrovic headed in from six yards.
Mitrovic spurned a great chance to double the lead as he raced onto a Moussa Sissoko through-ball only to shoot straight at Joe Hart.
Newcastle boss Steve McClaren reacted by putting his head in his hands, as if he knew a great chance might have passed his side by.
But really it might have mattered little, as City pulled one back before the break and then powered away courtesy of Aguero.
Aguero first shot narrowly wide from the edge of the area but then made no mistake three minutes before the interval as thumped in a header after Fernandinho had nodded down David Silva's floated cross.
City then really picked up the pace after the break and Aguero struck again as he took a Silva pass in his stride and beat Krul with aid of a deflection off Yoan Gouffran.
He completed his treble just a minute later - his third goal in the space of just eight minutes' playing time - with a classy finish, delicately chipped over the advancing Krul from a near-perfect De Bruyne pass.
From a position of strength just before break, Newcastle were rocking and their capitulation continued.
De Bruyne made it 4-1 after 52 minutes by lobbing Krul with a brilliant volley on the turn from a cross from impressive substitute Jesus Navas wide on the right.
Moments later it was 5-1 as Aguero took a touch to wrong-foot Mbemba on the edge of the area from a Silva pass and clinically despatched a low curling shot beyond Krul's reach.
Aguero then became the fifth player in Premier League history to score five goals in a match just after the hour when he turned in a De Bruyne cross from close range.
It was a blistering purple patch from Aguero and it came as some surprise when he was taken off by manager Manuel Pellegrini after 66 minutes, replacing him with Wilfried Bony.
Bony and Kelechi Iheanacho both had late chances but the job had been done by City in comprehensive fashion and Newcastle were probably pleased to escape the field without further damage.
Source : PA
Source: PA