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Here is an alternative take on Donu's argument: Removing the image of a section of $E_\Gamma$ allows one to regard a fiber of $E_{\Gamma}$ as a once-punctured torus $S$. (In order to construct a section, use the standard upper half-space model of the Teichmuller space of the tori, so that each marked torus is identified with the fundamental parallelogram $P$ with vertices $0, 1, \omega, \omega+1\in {\mathbb C}$. Then the section is given by the map $\omega\to 0\in P$.) Then $E_{\Gamma}$ is isomorphic to the quotient of the Teichmuller space $T(S)$ of $S$ by a finite-index torsion-free subgroup $Mod^o_S$ of the mapping class group $Mod_S$ of $S$. Now, this is a general fact (Deligne-Mumford, et al) that $T(S)/Mod^o_S$ is quasi-projective (for any Riemann surface of finite type). In the special case you are interested in, it seems that quasi-projectivity of $E_{\Gamma}$ was first proven by Kodaira (On compact analytic surfaces. II, III), at least, Shioda (On elliptic modular surfaces, 1972) attributes the result to him.