Applying PhD during the last year of master studies
You can definitely apply. If not now, then when?
The number of publications doesn't matter that much because the number is just a number; it doesn't reflect the complexity or difficulty of the research you did. I would fully expect that the publication resulting from your Masters studies will be more substantial - i.e., involve more work, with more robust results - than those you did during your Bachelor's.
If it still troubles you, remember there are people who do PhD studies without having published any papers in the past,