However, he will now stay home for treatment in an attempt to be fit for New Zealand's upcoming tour of Zimbabwe.
"Tim has suffered some cartilage damage to his left knee while preparing for the Champions League," New Zealand director of cricket John Buchanan said.
"He requires further assessment to determine the seriousness of the injury but initial signs indicate that he is unlikely to require surgery.
"A call on his availability for the Black Caps' tour of Zimbabwe will be made closer to the time."
Southee's performance of the year award was for his five wickets in eight balls, including a hat-trick, when New Zealand beat Pakistan by five wickets last December.