The answer is very strongly hinted at in Act 1 but certainly it is made explicit by the end of the play. At the beginning of the play, when we are introduced to a desperate Parris trying to work out what to do about his daughter, Betty, he questions Abigail about her reputation in the town. Note what he asks her:
Abigail, is there any other cause than you have told me, for your being discharged from Goody Proctor's service? I have heard it said, and I tell you as I heard it, that she comes so rarely to the church this year for she will not sit so close to something soiled. What signified that remark?
Of course, it is interesting to note Abigail's somewhat volcanic response as she goes to great lengths to testify to her own "good name" and to denigrate Goody Proctor.
When we see John Proctor and Abigail together it is clear that they have had an affair, which is why Abigail was thrown out of the house and why there is enmity between them.