If the distribution function has a step discontinuity at the Fermi surface, its derivatives are Dirac delta functions which reduce the integral to one over the Fermi surface. I will illustrate this for the simple case of a 2D system with a rectangular Fermi surface, but the full argument for 2D and 3D can be found in Haldane's Phys. Rev. Lett. 93, 206602 (2004) [arXiv version]. A related paper is X. Wang, D. Vanderbilt, J. R. Yates and I. Souza's Phys. Rev. B 76, 195109 (2009) [arXiv version]. (The rectangle is topologically equivalent to the circle, but makes it easy to work with an explicit coordinate system, thus making the problem concrete.)
We start with your Eq. (2),
$$\sigma_{xy}^{2D}=\frac{e^2}{\hbar} \int \frac{d\vec{k}}{(2\pi)^2}
\left( \frac{\partial f}{\partial k_y} \mathcal{A}_{k_x}-\frac{\partial f}{\partial k_x} \mathcal{A}_{k_y} \right) \tag{4}.$$
Now, assume a rectangular distribution function. A simple way to write one is
$$
f = \left[ \theta \left( k_x \right) - \theta \left( k_x -k_{\mathrm{F},x} \right) \right] \left[ \theta \left( k_y \right) - \theta \left( k_y -k_{\mathrm{F},y} \right) \right], \tag{5}
$$
which is constant and equal to 1 in the crosshatched area of the figure below, and vanishes outside it.

It of course follows that
$$
\frac{\partial f}{\partial k_x} = \left[ \delta \left( k_x \right) - \delta \left( k_x -k_{\mathrm{F},x} \right) \right] \left[ \theta \left( k_y \right) - \theta \left( k_y -k_{\mathrm{F},y} \right) \right], \tag{6}
$$
$$
\frac{\partial f}{\partial k_y} = \left[ \theta\left( k_x \right) - \theta\left( k_x -k_{\mathrm{F},x} \right) \right] \left[ \delta\left( k_y \right) - \delta \left( k_y -k_{\mathrm{F},y} \right) \right]. \tag{7}
$$
Substituting these expressions into (4) and carrying out integrals over the Delta functions we obtain
$$\sigma_{xy}^{2D}=\frac{e^2}{\hbar} \int \frac{dk_x}{\left( 2\pi\right)^2} \left[ \theta \left( k_x \right) - \theta \left( k_x -k_{\mathrm{F},x} \right) \right] \left[ \mathcal{A}_{k_x}|_{k_y=0} - \mathcal{A}_{k_x}|_{k_y=k_{\mathrm{F},y}} \right]\\
- \frac{e^2}{\hbar} \int \frac{dk_y}{\left( 2\pi\right)^2} \left[ \theta \left( k_y \right) - \theta \left( k_y -k_{\mathrm{F},y} \right) \right] \left[ \mathcal{A}_{k_y}|_{k_x=0} - \mathcal{A}_{k_y}|_{k_x=k_{\mathrm{F},x}} \right], \tag{8}$$
where the notation $f|_{x=0}$ indicates that $f$ is evaluated at $x=0$. Now it is just a matter of identifying the different terms with different paths in the figure, which yields
$$
\sigma_{xy}^{2D}=\frac{e^2}{\hbar} \left[ \int_{\Gamma_1} \mathcal{A}_{k_x} dk_x + \int_{\Gamma_2} \mathcal{A}_{k_y} dk_y + \int_{\Gamma_3} \mathcal{A}_{k_x} dk_x + \int_{\Gamma_4} \mathcal{A}_{k_y} dk_y \right]. \tag{9}
$$
Since $\Gamma=\Gamma_1+\Gamma_2+\Gamma_3+\Gamma_4$ is a closed contour we have
$$
\sigma_{xy}^{2D}=\frac{e^2}{\hbar \left( 2\pi\right)^2} \oint_\Gamma \vec{\mathcal{A}} \cdot \vec{dk}, \tag{10}$$
which matches your Eq. (3) up to a factor of $2\pi$, and agrees with Haldane's result in the article mentioned above. Finding the source of this discrepancy is left as an exercise.