Proof.
Write $Y = \mathop{\mathrm{lim}}\nolimits _{i \in I} Y_ i$ as a limit of algebraic spaces over a directed set $I$ with affine transition morphisms and with $Y_ i$ Noetherian, see Limits of Spaces, Proposition 70.8.1. We will use the material from Limits of Spaces, Section 70.23.
Choose a presentation $\mathcal{X} = [U/R]$. Denote $(U, R, s, t, c, e, i)$ the corresponding groupoid in algebraic spaces over $Y$. We may and do assume $U$ is affine. Then $U$, $R$, $R \times _{s, U, t} R$ are quasi-separated algebraic spaces of finite type over $Y$. We have two morpisms $s, t : R \to U$, three morphisms $c : R \times _{s, U, t} R \to R$, $\text{pr}_1 : R \times _{s, U, t} R \to R$, $\text{pr}_2 : R \times _{s, U, t} R \to R$, a morphism $e : U \to R$, and finally a morphism $i : R \to R$. These morphisms satisfy a list of axioms which are detailed in Groupoids, Section 39.13.
According to Limits of Spaces, Remark 70.23.5 we can find an $i_0 \in I$ and inverse systems
$(U_ i)_{i \geq i_0}$,
$(R_ i)_{i \geq i_0}$,
$(T_ i)_{i \geq i_0}$
over $(Y_ i)_{i \geq i_0}$ such that $U = \mathop{\mathrm{lim}}\nolimits _{i \geq i_0} U_ i$, $R = \mathop{\mathrm{lim}}\nolimits _{i \geq i_0} R_ i$, and $R \times _{s, U, t} R = \mathop{\mathrm{lim}}\nolimits _{i \geq i_0} T_ i$ and such that there exist morphisms of systems
$(s_ i)_{i \geq i_0} : (R_ i)_{i \geq i_0} \to (U_ i)_{i \geq i_0}$,
$(t_ i)_{i \geq i_0} : (R_ i)_{i \geq i_0} \to (U_ i)_{i \geq i_0}$,
$(c_ i)_{i \geq i_0} : (T_ i)_{i \geq i_0} \to (R_ i)_{i \geq i_0}$,
$(p_ i)_{i \geq i_0} : (T_ i)_{i \geq i_0} \to (R_ i)_{i \geq i_0}$,
$(q_ i)_{i \geq i_0} : (T_ i)_{i \geq i_0} \to (R_ i)_{i \geq i_0}$,
$(e_ i)_{i \geq i_0} : (U_ i)_{i \geq i_0} \to (R_ i)_{i \geq i_0}$,
$(i_ i)_{i \geq i_0} : (R_ i)_{i \geq i_0} \to (R_ i)_{i \geq i_0}$
with $s = \mathop{\mathrm{lim}}\nolimits _{i \geq i_0} s_ i$, $t = \mathop{\mathrm{lim}}\nolimits _{i \geq i_0} t_ i$, $c = \mathop{\mathrm{lim}}\nolimits _{i \geq i_0} c_ i$, $\text{pr}_1 = \mathop{\mathrm{lim}}\nolimits _{i \geq i_0} p_ i$, $\text{pr}_2 = \mathop{\mathrm{lim}}\nolimits _{i \geq i_0} q_ i$, $e = \mathop{\mathrm{lim}}\nolimits _{i \geq i_0} e_ i$, and $i = \mathop{\mathrm{lim}}\nolimits _{i \geq i_0} i_ i$. By Limits of Spaces, Lemma 70.23.7 we see that we may assume that $s_ i$ and $t_ i$ are smooth (this may require increasing $i_0$). By Limits of Spaces, Lemma 70.23.6 we may assume that the maps $R \to U \times _{U_ i, s_ i} R_ i$ given by $s$ and $R \to R_ i$ and $R \to U \times _{U_ i, t_ i} R_ i$ given by $t$ and $R \to R_ i$ are isomorphisms for all $i \geq i_0$. By Limits of Spaces, Lemma 70.23.9 we see that we may assume that the diagrams
\[ \xymatrix{ T_ i \ar[r]_{q_ i} \ar[d]_{p_ i} & R_ i \ar[d]^{t_ i} \\ R_ i \ar[r]^{s_ i} & U_ i } \]
are cartesian. The uniqueness of Limits of Spaces, Lemma 70.23.4 then guarantees that for a sufficiently large $i$ the relations between the morphisms $s, t, c, e, i$ mentioned above are satisfied by $s_ i, t_ i, c_ i, e_ i, i_ i$. Fix such an $i$.
It follows that $(U_ i, R_ i, s_ i, t_ i, c_ i, e_ i, i_ i)$ is a smooth groupoid in algebraic spaces over $Y_ i$. Hence $\mathcal{X}_ i = [U_ i/R_ i]$ is an algebraic stack (Algebraic Stacks, Theorem 94.17.3). The morphism of groupoids
\[ (U, R, s, t, c, e, i) \to (U_ i, R_ i, s_ i, t_ i, c_ i, e_ i, i_ i) \]
over $Y \to Y_ i$ determines a commutative diagram
\[ \xymatrix{ \mathcal{X} \ar[d] \ar[r] & \mathcal{X}_ i \ar[d] \\ Y \ar[r] & Y_ i } \]
(Groupoids in Spaces, Lemma 78.21.1). We claim that the morphism $\mathcal{X} \to Y \times _{Y_ i} \mathcal{X}_ i$ is a closed immersion. The claim finishes the proof because the algebraic stack $\mathcal{X}_ i \to Y_ i$ is of finite presentation by construction. To prove the claim, note that the left diagram
\[ \xymatrix{ U \ar[d] \ar[r] & U_ i \ar[d] \\ \mathcal{X} \ar[r] & \mathcal{X}_ i } \quad \quad \xymatrix{ U \ar[d] \ar[r] & Y \times _{Y_ i} U_ i \ar[d] \\ \mathcal{X} \ar[r] & Y \times _{Y_ i} \mathcal{X}_ i } \]
is cartesian by Groupoids in Spaces, Lemma 78.25.3 and the results mentioned above. Hence the right commutative diagram is cartesian too. Then the desired result follows from the fact that $U \to Y \times _{Y_ i} U_ i$ is a closed immersion by construction of the inverse system $(U_ i)$ in Limits of Spaces, Lemma 70.23.3, the fact that $Y \times _{Y_ i} U_ i \to Y \times _{Y_ i} \mathcal{X}_ i$ is smooth and surjective, and Properties of Stacks, Lemma 100.9.4.
$\square$
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