Code:
\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage{amsmath}
\begin{document}
\begin{align*}
J
&= J_0 + 2 m r^2
& \label{eq:asdf}\refstepcounter{equation}(\theequation)
&& \tilde{J}
&= J_0 + 2 m \tilde{r}^2 & \refstepcounter{equation}(\theequation)
\end{align*}
\eqref{eq:asdf}
\end{document}
Output:

I want to reference (1).

\labelafter\refstepcounter(although usingalign*and then using\refstepcounterby hand is pretty odd:-) – David Carlisle Oct 03 '14 at 14:51\section{foo}before your equation and you will see the\refpicks up the section number. The usage above is exactly like putting\lablebefore\captionin a figure, about which there are several answers on this site and elsewhere – David Carlisle Oct 03 '14 at 15:22\refstepcountersets the current label (which is why you need to do that first, as for undoing amsmath definition John beat me by a few seconds:-) – David Carlisle Oct 03 '14 at 15:32