The Pune franchise fought off Mumbai, Bangalore, Delhi and Hyderabad to get the 25-year-old, paying 145 million Indian rupees despite his limited availability for the Twenty20 competition.
With England hosting South Africa in a one-day series in May, Stokes is set to miss the final phase of the April 5-May 21 tournament, yet the bidding surged from his base price of 20 million rupees.
Pune owner Sanjiv Goenka told reporters that Stokes, now the most expensive overseas player in IPL history, would bring something new to the team for the 10th edition of the tournament.
"He's a complete player and he completes our squad. We've been lacking this one genre of player," he said.
"We knew he was going to be there for the first 14 games ... We pretty much knew we were not going to get him for below this price."
Tymal Mills, Stokes's England Twenty20 team mate, was snapped up for 120 million rupees by Royal Challengers Bangalore, who will look to benefit from the left-arm fast bowler's ability to combine great pace with economy.
All-rounder Chris Woakes was the third England player to get a hefty payday, going to Kolkata Knight Riders for 42 million rupees.
Other big-earners included New Zealand fast bowler Trent Boult and South Africa paceman Kagiso Rabada, who both went for 50 million rupees to Kolkata Knight Riders and Delhi Daredevils respectively.
England's limited-overs captain Eoin Morgan went to Kings XI Punjab for a relatively modest 20 million rupees.
Delhi Daredevils bought Australian paceman Pat Cummins for 45 million rupees, while compatriot Mitchell Johnson, who quit international cricket in 2015, returned to his former team Mumbai Indians for 20 million.
Owners mostly gave the cold shoulder to slow bowlers, with South African leg-spinner Imran Tahir, who tops both the one-day and Twenty20 bowling rankings, unsold.
Mohammad Nabi became the first Afghanistan player to be bought in the IPL with Sunrisers Hyderabad offering three million rupee for the all-rounder. They also bought Afghan leg-spinner Rashid Khan for 40 million rupees.
(Reporting by Amlan Chakraborty in New Delhi; editing by Ed Osmond)
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