Dhoni's India teammate Suresh Raina was the first preference for the other new team Rajkot, which is owned by Intex Mobiles. He will also get an identical Rs 12.5 crore by virtue of being the first player selected by the franchise.
Seven players of the suspended Chennai Super Kings, including Dhoni, were picked along with three others from the Rajasthan Royals, also banned from the league for two years.
The draft process was necessitated following the suspension of Chennai Super Kings and Rajasthan Royals from the IPL for two years in the wake of the 2013 spot-fixing and betting scandal.
The suspension was ordered by the Supreme Court-appointed Justice (retd) R M Lodha committee, which was formed to decide the quantum of punishment following the investigations.
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Off-spinner Ravichandran Ashwin was picked by Pune as their third choice and will get a purse of Rs 7.5 crore. New Zealand captain Brendon McCullum was Rajkot's choice.
Pune opted for South African batsman Faf du Plessis as their fifth and final player, while West Indian Dwayne Bravo was Rajkot's pick. Both players will get Rs 4 crore.
The draft pool only included players from Chennai Super Kings and Rajasthan Royals,. The two teams which have been barred from participation. The players not picked will now go to the general
IPL auction scheduled for February 6.
The next edition of the Twenty20 league will be held from April 9 to May 29.
The unsold players will now go to the players' auction to be held on February 6, said IPL chairman Rajeev Shukla.
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Another BCCI source said the salary details will be revealed on the website after the first trading window closes on December 31.
"Both the teams (who have each spent Rs 39 crore today) are now left with Rs 27 crore each from the total purse to form the rest of the team," he added.
Shukla said that a decision whether to invite Pakistan players to play in IPL was different from the bilateral series between India and Pakistan that is hanging in the balance.
"The series against Pakistan is different and including Pakistan players in IPL is different. We will have to discuss with the franchises. As far as the series against Pakistan is concerned the same situation prevails. We have got no communication from the government," he said.
Shukla said the opening game in the 9th season of IPL as well as the final will be played at the Wankhede Stadium in Mumbai on April 9 and May 29.
He also pointed out that two new teams have been bought and a title sponsor already found when asked about IPL's credibility taking a hit.
"You have seen two new teams have been decided upon. You know how many turned up (for tender process). Title sponsorship too has been decided," said Shukla.
"Whatever we had planned, we have got. We wanted Dhoni as we are a new franchise and want to build our brand and who better than Dhoni. He was an automatic choice. We have got the players we wanted," he said.
"We were targetting eight players and got players of our priority. Manoj Tiwari and Ashok Dinda, who play for our company, were consulted. We have already talked to two contenders for coach," he said while making it clear that Sourav Ganguly, an IPL Governing Council member, was not involved in the process though he is a partner in their Indian Super League football team Atletico de Kolkata.
"We had a strategy and we knew Dhoni will not be available. So Raina was a strong option. On the Rajkot pitch we need aggressive batsmen as well as strong bowlers. We needed to have a balanced team."
He said his team, though missing the first eight seasons' experience, will learn from past mistakes committed by the other teams.
"We are a new franchise while others have the advantage of playing in the first eight seasons. But we will learn from their mistakes. My personal twitter is flooded with tweets. We will be announcing the captain soon."