Summary: Depending on your legal status with your partner, you may or may not need to pay the 3% SDLT surcharge.
HMRC clarified the situation via a series of examples. I believe either example 1 or 2 apply to your case:
Example 1
Mr and Mrs S, a married couple, each own a residential property, with neither having any interest in the other’s property. They both live in the property owned by Mrs S: the property owned by Mr S is rented out. Mrs S is selling her property and they are jointly purchasing a new one, which will be their new main residence. Mr S will retain his rented out property.
The higher rates will not apply to the joint purchase by Mr and Mrs S of a new main residence. As they are married and have both lived in the property owned by Mrs S as their main residence they will both be treated as replacing their main residence.
Example 2
Mr P and Ms B, who are not married to one another, each own a residential property, with neither having any interest in the other’s property. They both live in the property owned by Ms B: the property owned by Mr P is rented out. Ms B is selling her property and they are jointly purchasing a new one, which will be their new main residence. Mr P will retain his rented out property.
The higher rates will apply to the joint purchase of a new main residence by Mr P and Ms B. As they are not married (or in a civil partnership) Mr P will not be treated as replacing his main residence as, even though he has been living in the property owned by Ms B, he has no interest in the property Ms B is selling.
The silver lining is that if you are charged the extra 3% SDLT, you and your partner might be eligible to claim back the 3% difference if both of you have sold your respective (share of) properties within three years of this purchase.