The award was announced following the Test between Six Nations champions Ireland and Tri-Nations champions South Africa at Croke Park, Dublin on Saturday.
Ireland won 15-10.
South Africa have enjoyed a silverware-laden 2009, emphatically claiming the Tri-Nations title for the first time in five years and winning a compelling British & Irish Lions series in the summer.
The world champions reclaim the IRB Team of the Year Award from New Zealand, having previously won the prestigious honour in 2004 and 2007, and for captain John Smit the Award is recognition of a fantastic team ethic.
"It's been a huge year for us and to top it off with a recognition like this, to secure the top prize is massive.
It was a huge ambition of many of the guys to beat the British & Irish Lions, it was a goal to be victorious so that was a great highlight for us during the year," said Smit.
"I'm very proud to be associated with these guys, it has become a family of guys and hopefully we can keep it going for another two years."
IRB chairperson Bernard Lapasset added: "It has been a compelling year of international Rugby. South Africa have demonstrated this year exactly why they are world champions, winning the Tri-Nations and a truly memorable Lions series."
In May, England captain Ollie Phillips was named IRB Sevens Player of the Year, while Aaron Cruden was named IRB Junior Player of the Year in June after leading New Zealand Under-20s to the IRB Junior World Championship title.
Australia's Debby Hodgkinson was named IRB Women's Personality of the Year in August, L'Aquila Rugby Club received the Spirit of Rugby Award in September and this month Francis Palmade received the IRB Referee Award for Distinguished Service.
Previous Winners of IRB Team of the Year :
2001 - Australia
2002 - France
2003 - England
2004 - South Africa
2005 - New Zealand
2006 - New Zealand
2007 - South Africa
2008 - New Zealand