Stokes also scored a supreme 135 not out in the 76-run last-wicket stand with Jack Leach to guide England to their gripping one-wicket victory over Australia in the third Ashes test at Headingley.
Those efforts helped England level the Ashes series, eventually drawn 2-2, which was not enough to wrestle back the urn.
Stokes was the only man to record over 1000 runs and claim 25 wickets or more across all international formats over the past 12 months – he had 1571 runs and 31 wickets.
Wisden editor Lawrence Booth wrote of Stokes: "Without him, this Almanack might have been another English hard-luck story. Instead, it's a celebration. Stokes is their all-weather cricketer, a giant come rain or shine. The next few years should be fun.
"Every so often, an England cricketer joins the national conversation. First among equals is W G Grace, because he put the sport on the map. But others have kept it there: Hobbs, Hutton, Compton, Botham, Flintoff, Pietersen and now Stokes. Of the three modern all-rounders, Stokes can be the greatest."
Following his match-winning performance in the World Cup final, Stokes was nominated for New Zealander of the year award. He was born in New Zealand and holds Māori ancestry. While he moved to England aged 12, his parents now live in Christchurch.
In 2017, Stokes played three one-day games and three Twenty20 matches for Canterbury after he was arrested for his part in an altercation outside a Bristol nightclub and was made unavailable for England selection.
The 28-year-old is the first England men's player to receive Wisden's top award since Andrew Flintoff in 2005. Indian captain Virat Kohli won it for the past three years.
Stokes told the Mirror: "It is an honour to be named the leading cricketer in the world by Wisden and follow in the footsteps of some great names.
"I was delighted to be named as one of their cricketers of the year in 2016, and this is an appreciated addition.
"2019 was a year I will never forget, sharing some incredible highs alongside my team-mates who helped and allowed me to perform in the way I did. It always has been and always will be a team game.
"While we wait to find out when we might next be able to play again it is nice to receive an award like this and take a moment to remember how much we enjoy playing and watching this game, and I'm glad I was able to play my part in that enjoyment last year. It was the summer of cricket."
Wisden named England pace bowler Jofra Archer, Australians Pat Cummins, Marnus Labuschagne, Perry and South Africa's Essex off-spinner Simon Harmer their five cricketers of the year.
Players can only be named among this group once in their respective careers.
Perry is the first non-England women's player to appear as one of the five, and the first female to achieve the double in a single year.
Meanwhile, a shirt worn by England wicketkeeper Jos Buttler in the World Cup final has raised more than £65,000 ($134,000) for two London hospitals.
