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Smith is in the middle of a rare slump in form and dropped behind Kohli after registering four single-digit scores at the halfway stage of the ongoing four-test series against India.
Kohli, who topscored for India in their eight-wicket thrashing by Australia in the series opener in Adelaide, has returned home for the birth of his first child.
India's stand-in skipper, Ajinkya Rahane, jumped to number six after his stellar hundred in the second test inspired the tourists to a series-levelling victory in Melbourne.
Australia's Pat Cummins remains the top-ranked test bowler, while compatriot Mitchell Starc jumped two places to enter the top five.
India spinner Ravichandran Ashwin (seventh) and quick Jasprit Bumrah (ninth) improved their top 10 positions after their impressive performance in the Melbourne test.