Sydney cricket fans will remember when Kohli similarly lost his temper in January 2012, presenting the SCG crowd with his middle finger as he walked off the field.
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The 31-year-old — who won the ICC Spirit of Cricket Award in January — was also spotted mocking the crowd on Sunday, imitating a drunk person.
Latham made his way back to the pavilion for 52 and the Black Caps were eventually dismissed for 235, seven runs short of India's first innings total. Shami ended the innings with 4/81 from 23.1 overs.
However, New Zealand got the last laugh, with Kohli dismissed cheaply late on day two. The Indian captain missed a straight delivery from all rounder Colin de Grandhomme, and was trapped LBW for 14.
Kohli has been ruthlessly criticised for his poor performances with the bat during the New Zealand tour. Although he's touted as the world's best batsman across formats, Kohli has endured the worst series of his 12-year international career.
The 218 runs Kohli scored across nine matches in New Zealand is the lowest he has ever achieved on a tour where he played all the three formats.
Kohli averaged 9.50 with the bat after four Test innings, his lowest ever in an away series. With scores of two, 19, three and 14, it's also the second time in his ten-year Test career he hasn't passed 20 in a series. This is only the fourth occasion where Kohli failed to pass 20 more than once in a run of seven innings.
Even tailender Shami scored more runs than his skipper during the two-Test series.
ABC Grandstand radio presenter Akash Fotedar tweeted, "The inability of the other batsmen to carry the load in (Kohli's) absence has made this a tough tour for India".
Kohli was recently dethroned at the world's No. 1 Test batsman, dropping to second below Australia's Steve Smith. He's one of only two batsmen ranked in the top ten for all three formats, alongside Pakistan's Babar Azam.
India is 6/90 at stumps on day two, leading by 97 runs.