KLM we did ! I'm a vegemite girl too and don't travel anywhere overseas without it. I too carry the tube of Vegemite just for ease of packing and no risk of broken glass.
I have never had an issue with customs anywhere in the world , including SA. For most countries the only food items that are usually prohibited are fruits / vegetables and some meats products. Processed products like Vegemite that have an ingredient label are fine.
I should probably add that we always declare it if the form requires it.
Cape Town airport we found particularly relaxed when it came to customs - we got ushered straight through...