The former Springbok international came off just before half-time and will have an operation later in the week.
The 33-year old has been an influential figure for Toulon so far this season, frequently starting alongside one of Jocelino Suta, Simon Shaw or Nick Kennedy, who will now all fill in for Botha in his absence.
Botha's injury will rule him out of the Round 5 and Round 6 Heineken Cup games as Toulon look to secure a top seeding for the quarter-finals, although they currently lead Pool 6 by five points ahead of Montpellier.
Toulon will also be without Botha for Top 14 clashes against Perpignan and Racing Metro amongst others.
Gilbert has released a new line of rugby cleats. The Gilbert Virtuo 8S is part of the exciting new product. Check it out.
The Barbarians are one of the top invitational rugby sides with a long history and classic rugby jersey.
The Nike Tiempo is a solid rugby cleat and one of few styles still made from full-grain natural leather.
The Lions get ready for their matches with this green training jersey. It's what the players wear. Get in the Gear!
A cool looking all black rugby cleat with the high performance adidas is known for. Get in the Gear!
Wear the crest of the British and Irish Lions on your t-shirt. A great look for the summer.
The Lions are ready to get their Australia tour underway. They arrive in Perth on Monday.
The New Zealand All Blacks training jersey for 2013/14. Get in the Gear!
The USA Rugby Pro Alternate rugby jersey is perfect for any fan of the Eagles. Get yours to wear during the summer Test matches.
The NEW All Blacks 2013/14 jersey has arrived at World Rugby Shop. Dare to wear the colors of the All Blacks.