The left-arm pacer who has been an automatic selection for Pakistan in all three formats of the game since his return to international cricket had hurt his right shin during the second Test in Abu Dubai.
Lions' allrounder Mulder has been included in the squad as a replacement for Wayne Parnell, who has been ruled out of the remaining ODIs against Bangladesh and the T20I series with a groin injury.
Star batsman Kane Williamson will captain the Black Caps on the India tour comprising three ODIs and as many T20 Internationals, starting on October 22.
Head (48 off 34) and Moises Henriques (62 off 46) had shared an unbeaten 109-run stand off 76 balls to fire Australia to a series-levelling win in just 15.3 overs in the second T20I in Guwahati on Tuesday.
Australia swept to a crushing 8-wicket victory over India in their second T20I on Tuesday, after Moises Henriques and Travis Head piled on an unbeaten 109-run partnership to level the 3-match series 1-1.
Rookie pacer Jason Behrendorff (4/21) ripped through the high-profile Indian batting to restrict the home team to a below par 118 in the second T20I at the Baraspara Stadium, Guwahati.
Moises Henriques and Travis Head built an unbeaten 109-run stand to help Australia beat India by eight wickets in the second T20 international in Guwahati.
Mohammed Shami believes the players share a great repertoire on a personal level which translates into their on-field performance.
Australia lost the first game in Ranchi after familiar batting woes but stand-in captain Warner said the team would not sit and worry much about the collapse.
The 22-year old also added that he has learnt a lot by playing with Aussie chinaman specialist Brad Hogg at Kolkata Knight Riders and is in regular touch with his childhood idol, Shane Warne.
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India have won seven matches in a row against Australia in T20Is, the men in blue have not lost in the shorter format versus the Kangaroos since September 28, 2012.
India are 1-0 up in the 3-match series after the win in Ranchi on Saturday, the hosts would look to seal the series in Guwahati before the two teams head to Hyderabad for the final encounter.
The India skipper also attributed the team's stupendous success in recent times to the team management's decision to pick format-specific players.
India beat Australia by 9 wickets (DLS method) to take the 1-0 lead in the three-match T20I series.
Paine, who has featured in four Tests and 26 ODIs for Australia, said he has no regrets despite not being picked up earlier.
The Indian players arrived in the city last evening following a short break after the five-match ODI series, but they were denied practice because of a downpour in Ranchi.
The men in blue boast of an impressive 9-4 head-to-head record against Australia in the shorter format of the game.