You can include an if statement check to prevent system message from showing up in the chat.
if 'messages' not in st.session_state:
st.session_state.messages = [{'role': 'system', 'content': 'You are a helpful assistant.'}]
for message in st.session_state.messages:
if message['role'] != 'system':
with st.chat_message(message['role']):
st.markdown(message['content'])