\documentclass{article}
\usepackage{amsmath}
\usepackage{xepersian}
\settextfont{Yas}
\setdigitfont{Yas}
\makeatletter
\newcommand\myeqnnum{\hbox{\refstepcounter{equation}\@eqnnum}}
\makeatother
\begin{document}
\begin{equation}
1+2=3
\end{equation}
\begin{align}
(x+y)(x-y)&\stackrel{\myeqnnum}{=}x^2-xy+yx-y^2\nonumber\\
&=x^-y^2
\end{align}
\begin{equation}
\mathbf{c}(t)=(r\cos t, r\sin t)
\end{equation}
\end{document}