Brought into the Australia side for Travis Head after the middle order batsman Tested positive for COVID-19, Khawaja was clearly relishing his latest comeback at the ground where his Test career began.
The 35-year-old made his debut in the 2011 Ashes Test at the SCG -- England's last Test victory on Australian soil -- but has been in and out of the side in the intervening 11 years.
He survived a scare in the morning session when he got an edge on a delivery from England spinner Jack Leach but the ball evaded wicketkeeper Jos Buttler and Joe Root was unable to hold the catch at first slip.
Khawaja made the most of his reprieve, picking the moments to unleash his stylish strokes and bringing up his ninth Test century with three runs through square leg just before the break. The lefthander will resume for the final session unbeaten on 102 alongside his captain Pat Cummins, who had pummelled a couple of fours straight down the ground in his 15 not out.
Khawaja and Steve Smith had batted through the opening session at the Sydney Cricket Ground to dash England's hopes of taking early wickets.
Broad finally broke the 115-run fourth wicket partnership when Smith edged the ball behind on 67 and then quickly despatched all-rounder Cameron Green for five, caught in the cordon.
England bowlers were again unable to ride the momentum, however, and it was not until the hour before tea that Alex Carey departed for 13, holing out in the deep off England captain Root's spin.
England's cause was not helped by an injury to all-rounder Ben Stokes, who was treated for "tightness" in his left side just before lunch with the team confirming that he would be unable to bowl for the remainder of the day.
The tourists are desperate for a good showing in Sydney after suffering heavy defeats in Brisbane, Adelaide and Melbourne to go 3-0 down in the five-match series. The fifth Test starts in Hobart on Jan. 14.
The rain, which heavily disrupted the opening day, largely stayed away but there were a couple of short breaks in the opening session when passing showers interrupted the sunshine.