Botha was cited for a dangerous charge on Lions prop Adam Jones in the fourth minute of the second half at Loftus Versfeld and was given a two week ban the following day by IRB judicial officer Alan Hudson.
Botha became the first of two Springbok forwards to be banned by the Canadian official the day after the Boks clinched the series with their 28-25 triumph. Schalk Burger was given an eight week suspension for gouging and is also missing from the third Test in Johannesburg on Saturday.
The Springbok coaches claimed that Botha was merely trying to clean out at a ruck when he charged into Jones. Jones suffered a dislocated shoulder, an injury which ended his tour.
Botha is now definitely ruled out of this weekend's third Test, leaving his Blue Bulls lock partner Victor Matfield looking for a new colleague in the second row.