Reverse the order of pause when used with a stack

Instead of using \pause I'd recommend using a key visible on as defined in the preamble of the following MWE. The trick is to enclose each level of stack in a scope environment, and pass the key visible on=<num> to the environment to set the overlay effects. I also had to redefine the \cellptr command in the drawstack package to prevent the top right arrow to wiggle between frames.

MWE

\documentclass{beamer}
\usepackage{tikz}
\tikzset{
  invisible/.style={opacity=0},
  visible on/.style={alt={#1{}{invisible}}},
  alt/.code args={<#1>#2#3}{%
      \alt<#1>{\pgfkeysalso{#2}}{\pgfkeysalso{#3}} % \pgfkeysalso doesn't change the path
  },
}

\usepackage[nocolor]{drawstack}
\renewcommand{\cellptr}[1]{
  \draw[<-,line width=0.7pt] (0,0) +(2,0) -- +(2.5,0) node[anchor=west] {#1};
}

\begin{document}
\begin{frame}
\begin{tikzpicture}
\begin{scope}[visible on=<4->]
  \stacktop{} \cellptr{top of stack}
  \separator
\end{scope}
\begin{scope}[visible on=<3->]
  \cell{c} \cellcomL{2};
  \separator
\end{scope}
\begin{scope}[visible on=<2->]
  \cell{b} \cellcomL{1};
  \separator
\end{scope}
\begin{scope}[visible on=<1->]
  \cell{a} \cellcomL{0};
  \separator
\end{scope}
\end{tikzpicture}
\end{frame}
\end{document}

Output

A solution with a simple tabular:

\documentclass[table]{beamer}
\usepackage{fontspec}
\usepackage{libertine}
\usepackage{array}
\usetheme{Malmoe}

\begin{document}
\begin{frame}{Stack with a tabular}\arrayrulewidth=1pt
 \begin{tabular}{@{} l | 
    >{\columncolor{black!10}\centering\rule[-2ex]{0pt}{5ex}}p{3cm} |@{} r}\cline{2-2}
    & \ldots & $\longleftarrow$ top of stack \\\cline{2-2} \onslide<3->
  2 &   c    &                   \\\cline{2-2} \onslide<2->
  1 &   b    &                   \\\cline{2-2} \onslide<1->
  0 &   a    &                   \\\cline{2-2}  
 \end{tabular}
\end{frame}
\end{document}

Another solution with a simple makebox and without holes:

\documentclass[table]{beamer}
\usepackage{fontspec}
\usepackage{libertine}
\usepackage{array}
\usetheme{Malmoe}
\newcommand\MBox[2]{\makebox[1em]{#1}~\fbox{\makebox[3cm]{\rule[-2ex]{0pt}{5ex}#2}}}

\begin{document}
\begin{frame}{Stack with Boxes}\offinterlineskip
\onslide+<1->{\MBox{}{\ldots}$\longleftarrow$ top of stack\\}
\only<3->   {\MBox2c\\}
\only<2->   {\MBox1b\\}
\only<1->   {\MBox0a}
\end{frame}
\end{document}