Can Shanghai enterprises only pay three insurances for employees without paying provident fund?

No, now the social security paid by the unit is a combination of five insurances, and pension, medical care, maternity, unemployment and work injury are paid together. The unit itself cannot choose insurance to pay. But individuals only need to pay pension, medical care and unemployment (agricultural registered permanent residence doesn't).

Further reading: How to buy insurance, which is good, and teach you how to avoid these "pits" of insurance.