The Delmas Magistrate's Court sentenced Themba Mvubu to life for the 31-year-old's murder, 20 years for being an accomplice to rape and 15 years for robbery, said Phumi Mtetwa of the Equality Project.
Two other men were acquitted of the attack on the well-known lesbian activist and former national women's football team player, whose body was found in an open field in KwaThema township last April.
Mvubu's conviction follows a 32-year sentence handed down in February to a fourth accused who pled guilty to murder, robbery and being an accomplice to rape but later retracted statements implicating the other three.
Simelane's sexuality was ruled out in the first sentencing as a motive in her killing but activists have linked the case to "corrective rape" in which lesbians are targets of sexual violence.
The judge in the second trial on Tuesday had noted that the accused had told co-attacker Mpithi to "do something" as Simelane knew him, Mtetwa said.
"We can only make an inference that part of the knowledge of who she was had to do with her sexual and gender identity," she said.
Emily Craven of the Joint Working Group activist network said a guilty verdict had been hoped for against all three accused but that there was relief that the case was over.
"We are just very happy that it's over. It gives a chance for Eudy's family to find some peace and move on with their life," said.
"At the end of the day, it's probably to my mind the first case followed by the hate crimes campaign in South Africa that's actually come to a conclusion. We can learn from this case."
In March, a new study by anti-poverty group Action Aid warned that South African lesbians were suffering rapes by men trying to "cure" their homosexuality.
South Africa is one of the world's most violent societies with fresh crime statistics released on Tuesday showing a rise of sexual offences by 10.4% with 27 750 rapes committed in six months.