The 23-year-old, who was playing in his first one-day international since August, took three wickets to trouble the visitors in a contest eventually abandoned due to the sodden conditions.
Shami claimed the scalps of both openers Aaron Finch (5) and Phillip Hughes (11) in the first six overs, before also dismissing danger man Shane Watson for just 14 as Australia posted 8-295.
India were 0-27 when the weather hit but Dhoni took the positives from Shami's showing with the ball.
"Shami is deceptive," he said. "He bowls quicker than you would think. What was important was he bowled full and the wickets he got, he was hitting the bails.
"That shows he was bowling the right length on this pitch. And at the death he was getting the yorkers in pretty consistently."
India will look to level the series, which Australia lead 2-1, when the fifth ODI commences in Cuttack on Saturday.