2 country issue

This is too complicated a matter for an in-depth analysis on this board, but your employer needs to check if UK PAYE withholding should be made (they could be penalised for not doing this), as a starting point. You are earning money in the UK and so should pay tax here, rather than South Africa. You need to register for Self-Assessment asap and file a 17/18 tax return (get a professional to do this, as they can look at things like when your tax residence status in the UK begins) and pay the 17/18 tax liability by the end of January.

You should get a tax refund in South Africa to help pay the UK liability (as the UK earnings shouldn't ordinarily be taxable there, but I am not an expect in South African tax). Your employer should also see if the South African withholding can stop (in a worse-case scenario withholding may be due in both countries, with you then having to reclaim the tax that ultimately isn't due in South Africa - a cash-flow nightmare that I have seen before).

This can be something of a can of worms, but don't just ignore this, as it will come back to bite you if you do. Talk to your employer in the first instance, as they may have other employees in similar circumstances and so may know how to take this forward.

I hope this helps.

Your employer has numerous legal obligations in England & Wales. Do you have a contract under English law? Are you getting your legal entitlements under English law? The primary liability is right here in the UK. Presumably you'll reclaim all the tax wrongly withheld in SA from UK source income.