Assume that you have two point charges $1$ and $2$ and the force on charge $2$ due to charge $1$ is $\vec F(r)_{\text{2 due to 1}} = F(r) _{\text{2 due to 1}}\,\hat r $ where $F(r)_{\text{2 due to 1}}$ is the component of the force in the $\hat r$ direction, pointing away from charge $1$.
To move charge $2$ an external force $\vec F(r)_{\rm external} = F(r)_{\rm external} \,\hat r$ must be applied where $\vec F(r)_{\rm external} + \vec F(r)_{\text{1 due to 2}}=0 \Rightarrow F(r)_{\rm external} = -F(r)_{\text{1 due to 2}}$.
Suppose that the external force causes a small displacement of charge $2$ equal to $\Delta \vec r = (r_{\rm final} - r_{\rm initial})\,\hat r$
The work done by the external force is approximately equal to
$\vec F_{\rm external}(r_{\rm initial}) \cdot \Delta \vec r = F_{\rm external}(r_{\rm initial}) \hat r \cdot (r_{\rm final} - r_{\rm initial})\,\hat r = F_{\rm external}(r_{\rm initial}) \times (r_{\rm final} - r_{\rm initial})$
This a general result and has made no assumption about the sign of the charges and the displacement of charge $2$.
Using this relationship it is easy to answer your question.
If the two charges are both positive then $F_{\rm external}(r_{\rm initial})$ is negative.
Bringing charge $2$ closer to charge $1$ means that $r_{\rm final} < r_{\rm initial}$ and so $r_{\rm final} - r_{\rm initial}$ is negative.
So the work done is the product of two negative quantities ie positive.
With the external force being a function of position the work done can be written as
$$\int^{r_{final}}_{r_{\rm initial}} \vec F(r)_{\rm external} \cdot d\vec r = \int^{r_{final}}_{r_{\rm initial}} F(r)_{\rm external}\,\hat r \cdot dr \,\hat r = \int^{r_{final}}_{r_{\rm initial}} F(r)_{\rm external}\, dr$$
with the sign of $dr$ being dictated by the limits of integration.
Within this site there are a number of questions about using the integral to find the work done and getting the wrong sign for the answer.
Almost all the errors are due to using $-dr$ instead of $dr$ within the integral and/or including $\cos \pi$ when evaluating the dot product, eg link 1, link 2, etc.