The newly crowned 800m world champion has had medical tests following doubts about whether she is actually female.
Athletics' world governing body (IAAF), demanded the test three weeks before the World Championships and Lewis says Semenya should have been withdrawn.
"The South African federation should have dealt with it," said Lewis.
The IAAF said the teenager was first asked to undergo a gender test after she posted a world leading time of one minute, 56.72 seconds at the African junior championships in July.
To put it out in front of the world like that, I am very disappointed in them because I feel that it is unfair to her
The test was never conducted and Semenya was allowed to compete at the World Championships in Berlin.
However, the South African athletics federation denied there were concerns over Semenya stating: "We would not have entered her in the female competition if we had any doubts."
The IAAF was then roundly criticised for announcing Semenya would have to take a gender test just hours before the 800m final.
Semenya went on to win in Berlin in one minute, 55.45 seconds, the year's fastest time, a personal best and a national record.
"Here is an 18-year-old young woman, because that's what she feels she is, let down every step along the way... I think the federation let her down," added Lewis.
"It is your fault," he said of the South African athletics federation.
"She is your athlete in your country and you didn't deal with this before.
"To put it out in front of the world like that, I am very disappointed in them because I feel that it is unfair to her.
"Now, for the rest of her life she'll be marked as 'the one'."
Medical experts are still examining the results of the tests, with the conclusions expected in November and BBC Sport understands tests are likely to show Semenya has an intersex status.
South African President Jacob Zuma decried the invasion of Semenya's privacy and what he called the violation of her rights.
Subsequently the country's minister for woman and children Noluthando Mayende-Sibiya has filed a complaint with the United Nations over the IAAF's handling of the case.
She has accused the organisation of a "blatant disregard" for the athlete's "human dignity" and called on the UN Division for the Advancement of Women to investigate.
Meanwhile, South African sports minister Reverend Makhenkesi Stofile has reacted furiously to the idea Semenya could be banned, warning of a "third world war" if the row over her sex stops her competing.
"Neither Caster nor her family deserves this humiliation. None of them have done anything wrong. And we appeal that they be left alone," said Stofile.