Smith strolled to the crease at 55-2 after both openers fell victim to Overton. The classy right-hander was a batsman inspired - even by his lofty standards.
The fidgeting genius dispatched his third ball through the covers for four and continued to attack anything that was overpitched. He passed 50 in 58 deliveries.
Smith was sensible, leaving good balls and rotating the strike, while Khawaja struggled to score freely.
Smith was superb with his timing, helping a Stuart Broad bouncer over fine leg for six and delighting in the veteran's look of disbelief.
Smith was stoic when struck with the final delivery before tea, wearing a rearing ball from Overton on the gloves and grille then attentively ensuring it didn't dislodge the bails. Root, having failed with the bat on day one, successfully referred a lbw shout to dismiss Cameron Bancroft but otherwise had a substandard day in the field.
The visiting captain bizarrely failed to pick up a thick edge that Khawaja offered on 28 at 125-2; the ball careered through the slips cordon as Root moved the wrong way then haphazardly flung his arm out.
Root was also criticised by commentators for his bowling changes and field placings, especially the fact that Smith was on 47 when he faced Jimmy Anderson for the first time in the match.
Khawaja also went close to falling to Overton for a duck, with the paceman throwing himself to the left and almost reeling in a stunning one-handed return catch.
Earlier, Malan (140) and Bairstow (119) produced England's highest fifth-wicket partnership in a Test against Australia.