The four-test series between the world's top two teams witnessed considerable acrimony after Smith gestured to his dressing room for assistance on whether to review an umpire's lbw decision against him in the second test at Bengaluru.
Smith, who did not review, later admitted to the "brain fade" but his team dismissed Kohli's charge that they had repeatedly resorted to the practise in the match won by India to level the four-match series for the Border-Gavaskar Trophy.
"It's really offensive," Saker told reporters. "It's probably the worst thing you can be called is cheats, that's an offensive thing.
"We've never done anything like that and we never will."
The former England bowling coach said the Australian dressing room was surprised when Smith made the gesture.
"It's pretty much absurd I think. When Steven Smith did look up, we were more horrified than anyone else because we'd never seen that before," Saker said.
"We haven't got any elaborate sign system and when he did do that it was quite a surprise to us."
Australia batsman Peter Handscomb, who advised Smith to seek dressing room input from non-striker's end, blamed the fiasco on his own inexperience.
"(I was) just completely unaware that you couldn't do that," the 25-year-old said of his suggestion that goes against Decision Review System (DRS) protocols.
Despite the row, the International Cricket Council (ICC) opted not to level any charge against either Smith or Kohli, whose public outburst could also have been considered a breach of code of conduct.
The teams renew their rivalry when the third test gets underway at Ranchi on March 16 and Saker dismissed suggestions that Kohli had gone down in Australia's estimations.
"We respect him as a player, he's an amazing player and his passion and the way he wanted to get his team up was quite evident out on the ground," the 50-year-old said.
"There are times when you think he might have crossed the line, but a lot of teams have done that, and leaders have done that."
Former India captain Sunil Gavaskar, however, criticised the ICC for not taking action against Smith.
"It can't be that some countries get favourable treatment and some countries do not get favourable treatment," Gavaskar told NDTV channel.
The Border-Gavaskar Trophy was named in honour of the 67-year-old, the first batsman to amass 10,000 runs in test cricket, and former Australia captain Allan Border, who was the second.
(Reporting by Amlan Chakraborty in New Delhi; Editing by John O'Brien)
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