siunitx and alignat?

Something like this:

\documentclass{article}
\usepackage{amsmath,siunitx}
\begin{document}

\begin{alignat*}{4}
& I_{A}           && = \mathit{SSA}/\mathit{SST}  && ={} &\SI{99,25}{\percent}&\\
& I_{B}           && = \mathit{SSB}/\mathit{SST}  && = &\SI{0,35}{\percent}&\\
& I_{\mathit{AB}} && = \mathit{SSAB}/\mathit{SST} && = &\SI{0,40}{\percent}&
\end{alignat*}

\end{document}

The extra {} is to make the spacing after the last = correct.

BTW: since you did not share a full minimal example, I did not replicate getting comma into the output. Please always share a full minumal example instead of sniplets.

Here's a solution that uses an array environment.

\documentclass[12pt]{article}
\usepackage[english, italian]{babel}

\usepackage{array}
\newcolumntype{C}{>{{}}c<{{}}}  % col. type for binary and relational operators
\newenvironment{myarray}[1]{%  % define a customized 'array' environment
   \setlength\arraycolsep{0pt}
   \renewcommand\arraystretch{1.25}
   \begin{array}{#1}}{%
   \end{array}}

\usepackage{siunitx}
\sisetup{unit-mode = text, output-decimal-marker={,}, 
         detect-mode, detect-shape, 
         group-digits = integer, binary-units=true}

\begin{document}
\[
\begin{myarray}{@{} lClCr @{}}
 I_{A} &=& \mathit{SSA}/\mathit{SST} &=& \SI{99,25}{\percent}\\
 I_{B} &=& \mathit{SSB}/\mathit{SST} &=& \SI{0,35}{\percent}\\
 I_{\mathit{AB}} &=& \mathit{SSAB}/\mathit{SST} &=& \SI{0,40}{\percent}
\end{myarray}
\]
\end{document}

eddit: sorry but at uploading my answer, i was interrupted ... and than Mico overtake me for one minute with similar idea ... however, some details the mine answer are different (and simpler?):

\documentclass{article}
\usepackage{amsmath,siunitx}

\begin{document}
\[
\setlength\arraycolsep{1pt}
\begin{array}{llcS[table-format=2.2,
                   table-space-text-post={\,\%},
                   output-decimal-marker={,}]<{\,\%}
             }
I_{A}           & = \mathit{SSA}/\mathit{SST}  & = & 99.25  \cr
I_{B}           & = \mathit{SSB}/\mathit{SST}  & = &  0.35  \cr
I_{\mathit{AB}} & = \mathit{SSAB}/\mathit{SST} & = &  0.40  \cr
\end{array}
\]
\end{document}