One option:
\documentclass{beamer}
\usepackage{amssymb}
\newlength\mylen
\newlength\mylena
\newlength\mylenb
\newcommand\R{\mathbb{R}}
\newcommand\bL{bL}
\newcommand\Div{Div}
\newcommand\getmaxlength[2]{%
\settowidth\mylen{#1}%
\settowidth\mylena{#1}%
\settowidth\mylenb{#2}%
\ifdim\mylenb>\mylena\relax
\setlength\mylen{\mylenb}
\fi%
}
\newcommand\Replace[2]{%
\getmaxlength{#1}{#2}%
\makebox[\mylen][c]{#2}%
}
\begin{document}
\begin{frame}
\onslide<1,2>{
\[
x+
\only<1>{\mathrm{Trace}M}
\only<2>{\Replace{$\mathrm{Trace}M$}{$y$}}
=z
\]
}
\onslide<3,4>{
\[
x+
\only<3>{\Replace{$\mathrm{Trace}M$}{$y$}}
\only<4>{\Replace{$y$}{$\mathrm{Trace}M$}}
=z
\]
}
\onslide<5->{
Comme l'application d\'eterminant est diff\'erentiable et que sa diff\'erentielle en l'identit\'e est l'application trace, alors $p.p.\, y\in\R^3,\,$:
\[
\only<5>{\mathrm{det}(D_y\Phi(t,y))}
\only<6->{\Replace{$\mathrm{det}(D_y\Phi(t,y))$}{$|J(t,y)|$}}=1+t\,\only<5>{\mathrm{Trace}(D_yV(y))}
\only<6->{\Replace{$\mathrm{Trace}(D_yV(y))$}{$\Div_y V(y)$}}
+t\,\epsilon_1(t,y),\,\epsilon_1(t)\xrightarrow{\bL^{\infty}}0.
\]
}
\end{frame}
\end{document}

The main command is
\Replace{<text1>}{<text2>},
which typesets but reserving the space used by . For expressions in math mode, the argument(s) should be enclosed in $...$.
Not related to the question, but please don't use $$...$$ in LaTeX documents; use \[...\] instead; see Why is \[ ... \] preferable to $$ ... $$?.
\bLand\Div? Please provide complete, auto-contained examples. – Gonzalo Medina Mar 14 '14 at 16:52