System Role Messages to Assistant for Function Calling

As per the Official Function Calling Cookbook, we can add System Role messages for Chat Completion model like this:

messages = []
messages.append({"role": "system", "content": "Don't make assumptions about what values to plug into functions. Ask for clarification if a user request is ambiguous."})
messages.append({"role": "user", "content": "What's the weather like today"})
chat_response = chat_completion_request(
    messages, tools=tools
)
assistant_message = chat_response.choices[0].message
messages.append(assistant_message)
assistant_message

But, as Messages in Assistant APIs only support User and Assistant Role, how can I add the above System Context messages in Assistant API?

I know that to give system context messages in Assistant I have to use Instructions while creating Assistant but I tried to pass some of the instruction for Function Calling there but wasn’t successful.