Then, you'll need to completly emulate the thing. The idea is that you loop over all your instances, incrementing an instance_id, send it to the shaders, then call to glDrawElements.
You can see this for example: https://www.opengl.org/sdk/docs/man/html/glDrawElementsInstancedBaseInstance.xhtml
The thing is that you'll need to upload to the shaders the instance_id for each draw call. So, it might be more efficient to do it in a different way.
Also, if you have VAO (https://www.khronos.org/registry/webgl/extensions/OES_vertex_array_object/), then I highly suggest you to use them. Sending pointers to GL will be far more efficient, since you'll do them only once (at the VAO creation). It might also be possible to use both VAO and the kind of BaseInstance emulation by using dynamic VBO and only update the required part of the buffer (the attrib array that might vary).
Hope that helps.