Manchester United, playing on Saturday afternoon, had beaten Burnley 1-0 at Turf Moor courtesy of an Anthony Martial goal to cut City’s lead to nine points.
But in the late kick-off, Pep Guardiola’s men made sure that their cushion was reestablished with an ultimately comfortable win over Rafael Benitez’s struggling Newcastle United side.
Aguero’s first came after 34 minutes when he nudged home Kevin de Bruyne’s shot. He got his second from the penalty spot in the second-half after Javier Manquillo tripped Raheem Sterling.
Four minutes later, Jacob Murphy halved the deficit but Aguero made sure of the points seven mintues from time. It was his 11th hat trick for City and his second of the season following his haul in the 6-0 win at Watford on 16 September.
"We needed this win after last week’s loss at Liverpool," Aguero told BT Sport. "It's a long season though and we've not won anything yet."
Guardiola added: "We need 10 more wins to be champions. It was important how we reacted at 2-1, we didn't panic."
Chelsea rose one place to third after a 4-0 romp at Brighton. Belgium international Eden Hazard scored twice and there were goals too for Willian and Victor Moses.
It was Chelsea’s first victory in three games following draws with Arsenal and Leicester City.