Different name in passport and bachelor certificate

If the name on the degree certificate is different from your passport, then MoM will not recognise it as your degree. If a degree is needed for S-Pass approval, your application will be rejected. (Please note that a university degree is not required for an S-Pass - university degree holders should normally apply for an EP!)
If this is indeed your own degree certificate, you should submit proof that it is (e.g. an official statement from your home country authorities that both writings are allowed and synonymous) or get another certificate with the correct name.

You did not mention what was the reason that it caused difference between passport and in your bachelor certificate. The reason I'm asking is, there is a possibility for case of a married lady where after marriage her surname/last name changed to her husband's surname. In that case you must have court's affidavit and marriage certificate to prove the change. Then you don't need to be worried.

If there is some other reason, then if you have any valid supportings then you can provide to MoM or would have given already at the time of submission.
MoM is very strict and possibility of rejection may happen. So, take immediate precaution which Beppi already mentioned what to do in his response.