"Following a medical assessment it was decided that he should undergo a scan to determine the extent of the injury.
"He had the scan on Tuesday morning that confirmed a presence of a further muscle injury to his right thigh which will require three-to-four weeks of rehabilitation which means he will miss the rest of the tour.
"I am especially disappointed for Leigh as he worked so hard to come back from the setback at the start of the tour but he has proven his strength of character by the way that he is handling the news and we wish him a quick recovery."
It caps off a very disappointing 24 hours for the British & Irish Lions camp, with Halfpenny's withdrawal following that of flanker Stephen Ferris yesterday due to a knee ligament injury.
"Leigh will travel with us to Cape Town and then return to the UK to continue his rehabilitation with the Cardiff Blues," McGeechan added.
"We will not be replacing Leigh as we have enough cover for his position amongst the group of players that we have."
Tour manager Gerald Davies said: "We are obviously very disappointed that Leigh has sustained a further injury and we understand that this must be particularly frustrating that this has happened a second time, especially for a young man embarking on his rugby career but we wish him well for his rehabilitation."