You have to avoid going in horizontal mode, which \rule does.
\documentclass[a4paper]{article}
\makeatletter
\newlength{\@fnruleindent}
\AtBeginDocument{
\settowidth{\@fnruleindent}{\textsuperscript{1}}
\addtolength{\@fnruleindent}{-\parindent}
\setlength{\@fnruleindent}{-\@fnruleindent}
}
\def\footnoterule{%
\kern -3\p@
\moveright\@fnruleindent\vbox to.4\p@{\hrule \@width .4\columnwidth}
\kern 2.6\p@
}
\makeatother
\begin{document}
abc\footnote{abc}
\end{document}
This works for footnote numbers up to 9. If you have more footnotes use
\settowidth{\@fnruleindent}{\textsuperscript{11}}
However I don't think it's a good idea.
According to Tschichold, the footnote rule should be the whole line width or absent. Other typographers disagree.