Botha was given a yellow card for repeated infringements by Lewis later in the first half of the 32-12 defeat to the All Blacks, but will now miss the remainder of South Africa's defence of the Tri-Nations title they took from New Zealand last summer.
Botha received an eight week ban in 2003 when he was cited for "attacking the face" of the Wallaby hooker Brendan Cannon and then picked up a two week suspension for his "dangerous charge" on British & Irish Lions prop Adam Jones last year that left the Welsh international with a dislocated shoulder.
Botha's ban came six days before his team mates have to face the All Blacks again in Wellington. He immediately apologized to Cowan and his team mates after hearing the decision.
Botha has apologised to his team-mates after being banned for his head butt on New Zealand scrum-half Jimmy Cowan.
"I sincerely regret the incident. I have let my team, my country and family down and I have done an injustice to the Springbok jersey and what it stands for," said Botha.
"I apologise to Jimmy Cowan and the New Zealand rugby public for what happened. Rugby is a physical sport but it has to be played within the boundaries and spirit of the law.
"I truly regret my actions and will make sure that I put the extended time away from the game to positive use and return to playing with the right attitude".
South Africa's national teams' manager Andy Marinos, spoke of the South African Rugby Union's disappointment at the actions of the 68-times capped forward.
"SARU views any incident of foul play in a very serious light. Bakkies remains an important player in Springbok rugby and I have discussed with him the extent of his actions and the implications it could have on the team, himself personally and his family," former Wales centre Marinos said.