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.
In-form Indian batsman Ajinkya Rahane was the second choice for Pune, while Rajkot opted for Ravindra Jadeja in the same position. Both players will be entitled to a purse of Rs 9.5 crore per year.
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.
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.
In the fourth spot, both the teams opted Australians with Steve Smith (Rs 5.5 crore) going to Pune and James Faulkner (Rs 5.5 crore) going to Rajkot.
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.
Out of this lot, Rahane, Faulkner and Smith had represented the Royals last year while the rest belonged to Super Kings. A total of 50 players from both suspended teams were available to be chosen in the draft.
The unsold players will now go to the players' auction to be held on February 6, said IPL chairman Rajeev Shukla.
"The salary of players as per their contract with their former teams will be protected. The upper limit will be deducted from the total purse of Rs 66 crore. All will be put up on the website," Shukla told a media conference after the draft.
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 on Tuesday) are now left with Rs 27 crore each from the total purse to form the rest of the team," he added.
"There are no catchment areas for the two teams," said Shukla.
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.
"The first trading window is to be held from December 15 (today) to December 31, the second one is from January 11 to 22, 2016 and the third one (after the players' auction) from February 8 to 19. The franchises' workshop will be held on January 13 and 14 in Srinagar," he said.
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.
Meanwhile, Pune franchise representative Subroto Talukdar, said that what was planned by his team had been accomplished at the draft, including the picking of Dhoni as their first choice.
"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.
"The name of the team and logo will be announced next week. We work out of Kolkata, so shifting to Pune will take some time. But we have the experience of running a team in ISL."
Rajkot franchise owner Keshav Bansal also sounded pleased with his team's picks.
"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."
"The BCCI has a fantastic senior management team, the chairman is fantastic, the president is fantastic and we have full faith in them," he added.
Teams Pune's picks: Mahendra Singh Dhoni, Ajinkya Rahane, Ravichandran Ashwin, Steve Smith, Faf du Plessis.
Team Rajkot's picks: Suresh Raina, Ravindra Jadeja, Brendon McCullum, James Faulkner, Dwayne Bravo.
— IndianPremierLeague (@IPL) December 15, 2015