The feisty right-armer has generally struggled for wickets, but has nonetheless been a major figure in India's long tour of Australia due to his strained relationship with the home side.
Harbhajan first clashed with the Australians in the second Test in Sydney, after which he was suspended for three Tests for allegedly racially abusing Andrew Symonds, a decision later overturned by an International Cricket Council appeal hearing.
Australia were not happy with the decision and tensions again surfaced in the tri-series clash in Sydney on Sunday, with the Indians accusing Matthew Hayden, Symonds and Ricky Ponting of provoking their players during the match.
On Tuesday, Hayden inflamed matters when he called Harbhajan an "obnoxious weed" on Australian radio.
Dhoni dismissed suggestions the controversies had impacted on Harbhajan's performances and said he would be a major figure in the upcoming tri-series finals against the Australians.
In a series dominated by the bowlers, Harbhajan has claimed just five wickets in games at 39.00, with a run rate conceded per over of 4.31.
Speaking after Tuesday's win over Sri Lanka that ensured India a berth in the tri-series finals, Dhoni said Harbhajan was bowling better than those statistics suggested.
"I think Harbhajan has done really well in the series so far, especially in the last game (against Australia)," Dhoni said.
"He bowled during the power plays and with field restrictions.
"He's not getting loads of wickets but you can see his contribution is very important."
Although India lodged a written complaint over Australia's "provocative" on-field behaviour after Sunday's game, team manager Bimal Soni said Wednesday they would not be taking any action over Hayden's latest taunts.
"We want to play cricket, and it is all in our letter to the match referee, and with what Hayden said our stance is vindicated," Soni said.
"This sort of thing should not happen but we've decided to take it in our stride and want to get on with preparing for the finals."
Meanwhile, Indian officials called for an end to the sledging between the sides, after Ishant Sharma was fined 15 percent of his match fee over a verbal clash with Symonds on Sunday.
India claim Sharma was provoked by the Australians and Board of Control for Cricket in India secretary Niranjan Shah told Indian television on Tuesday night that it had got "out of hand".