Let $\displaystyle f(z)=\frac{e^{iz}}{z}$, $z\in \mathbb{C}$. Then, for $R>\varepsilon>0$, Cauchy's Integral Theorem guarantees that
$$\begin{align}
0&=\int_\varepsilon^R \frac{e^{ix}}{x}\,dx +\int_0^{\pi/2}\frac{e^{iRe^{i\phi}}}{Re^{i\phi}}\,iRe^{i\phi}\,d\phi+\int_R^\varepsilon \frac{e^{-x}}{ix}\,i\,dx+\int_{\pi/2}^0 \frac{e^{i\varepsilon e^{i\phi}}}{\varepsilon e^{i\phi}}\,i\varepsilon e^{i\phi}\,d\phi\\\\
&=\int_\varepsilon^R \frac{e^{ix}}{x}\,dx -\int_\varepsilon^R \frac{e^{-x}}{x}\,dx-i\frac\pi2+O(\varepsilon)+O\left(\frac1R\right)\tag1
\end{align}$$
Taking the real part of both sides of $(1)$ and integrating by parts the integral $\int_\varepsilon^R \frac{e^{-x}}{x}\,dx$ with $u=e^{-x}$ and $v=\log(x)$, we find
$$\begin{align}-\int_x^R \frac{\cos(x')}{x'}\,dx'&=\log(x)-\int_\varepsilon^R e^{-x}\log(x)\,dx+\int_\varepsilon^x\frac{\cos(x')-1}{x'}\,dx'\\\\
&-\log(\varepsilon) -e^{-R}\log(R)+e^{-\varepsilon}\log(\varepsilon)+O\left(\frac1R\right)+O(\varepsilon)\tag2
\end{align}$$
Letting $R\to\infty$ and $\varepsilon\to 0$ in $(2)$ yields
$$\text{Ci}(x)=\log(x)+\gamma+\int_0^x \frac{\cos(x')-1}{x'}\,dx'\tag3$$
whereupon rearranging $(3)$ yields the coveted relationship.
Alternatively, we can use either the Laplace Transform or "Feynman's Trick" to show that
$$\int_0^\infty \frac{\cos(x)-e^{-x}}{x}\,dx=\int_0^\infty \left(\frac{x}{x^2+1}-\frac1{x+1}\right)=0\tag4$$
Starting with $(4)$, is tantamount to starting with the real part of $(1)$ and we are done.