Allan Donald will be the head coach of the side, while Rob Walters comes on board as assistant coach and will be the fitness trainer and fielding coach of the team.
Praveen Amre, meanwhile, would continue to be the assistant coach.
However Mathews won't be available during Pune Warriors' away match against Chennai Super Kings as Tamil Nadu government has decided against allowing any of the Lankan players take part in IPL games in Chennai.
"It's a great honour to be offered the captaincy of the Pune Warriors and I am grateful to the team management and franchise owners for the faith shown in me.
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"For me personally this is a great chance to gain leadership experience working with a multi-national squad and a very exciting opportunity given the enormous talent within our young squad," said Mathews.
Welcoming the Sri Lankan as the skipper of the Pune outfit, Sushanto Roy, Managing Director of Sahara Adventure Sports Limited, said the side would be benefitted by his leadership abilities.
"All the senior players in the team are happy with the choice and it is a joint decision taken by the senior players and team management. We now have a correct mix of youth and experience to launch an aggressive IPL season 6 campaign under the leadership of Mathews," he added.