Botha was caught on camera as he dived on Cowan in the opening minute Saturday night's Test.
Although the incident was apparently not seen by match officials, the big lock was later yellow-carded for a ruck infringement and the All Blacks scored 10 points while he was off the field on their way to a 32-12 victory.
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He was cited for "striking with the head following a tackle on All Blacks' halfback Jimmy Cowan," the SANZAR (South Africa, New Zealand, Australia Rugby) commissioner Scott Newland said.
Cowan, who had moments earlier impeded the big South African as he chased loose ball, was not injured.
It is not the first time the South African has been in trouble with the rugby judiciary.
The Bulls player missed this year's Super 14 play-offs after being suspended for a month on a reckless charge, and he received a two-week ban for the same offence against the British and Irish Lions last year.
He also missed three weeks of last year's Super 14 for striking and in 2003 he was suspended for eight weeks after allegedly spitting at, biting and eye-gouging Australian hooker Brendan Cannon.
