Smith, who moved up from number four following David Warner's retirement, made 12 and 11 not out in the series opener against West Indies, which Australia won inside seven sessions.
Warner and Khawaja had played junior cricket together and shared a great chemistry at the top of the order, and McDonald said Australia would let the new opening partnership develop the same kind of rapport.
"I suppose it's more just the connection of Usman and Smudge (Smith) over time," McDonald said.
"We've seen Davey and Usman's connection and then the partnerships that they've been able to produce. They're world-class performers at the top of the order and we think Steve Smith is one of the best problem-solvers in the game.
"We've said that leading into this and it makes sense for us that he's at the top."
West Indies fast bowler Shamar Joseph, who made his test debut in Adelaide, dismissed Smith with his first ball in international cricket and claimed 5-94 in the first innings.
Another debutant, Justin Greaves, claimed 2-36 but McDonald was confident Australian batters would do better in the day-night second test in Brisbane, beginning on Thursday, having gained some familiarity with the new West Indies attack.
"Sight unseen is always difficult for batters, when you haven't seen someone and gotten used to their rhythm and the cues they present," McDonald said.
"Sometimes you do get drawn into shots that potentially you don't play.
"We feel as though now that there's less unknowns going into the second test match, we've had a good look at them, a lot of those little decision-making errors that may have crept in I think will iron themselves out."
