Karabo Mokoena's mother wept as she arrived at the hearing.
A widespread online campaign to find Mokoena was called off on Wednesday when her father confirmed her death.
The case has sparked a fierce debate about the levels of violence faced by women in South Africa
Police are still waiting for DNA tests to confirm the identity of the body, which they said was "badly burned".
The case has prompted an outpouring of anger and grief in South Africa, mostly by women who took to social media to share stories of abuse they had suffered at the hands of their partners.
The suspect will remain in custody after the case was adjourned until 24 May, local Jacaranda News reports.
The hashtags #RIPKarabo and #MenAreTrash have been trending across the country as women call for an end to violence against them.
South Africa has among the highest rates in the world for the rape and murder of women.
More than 40,000 cases of rape are reported every year, figures which are thought to only represent a fraction of actual attacks.
Being a woman in South Africa is like being trapped in a locked room - you can hear someone walking outside and you know someone will come one day and you won't be able to stop them.
There is nothing you can do to stop him.
Nothing can protect you - not the pepper spray in your bag, not the self-defence classes you got as a gift for your birthday when your breasts developed, not travelling in groups, not the NO you've been taught to say should that day come - nothing.
It is learning to be "vigilant" before you even know what it is to feel safe.
It is feeling unsafe everywhere, all the time.
African societies are built on patriarchy - every young girl grows up knowing that a man is the head, that he is powerful, that he is a go-getter, a conqueror. We are taught to admire these very traits about you, and I do. But dear God I am afraid of you - and with good reason.
The statistics in this country are not in my or any woman's favour. They say that one day I, or someone I know, will be your victim.