You have to change the options for \rule:
\documentclass[12pt, a4paper]{scrreprt}
\usepackage{lipsum}% only for dummy text
\usepackage{xcolor}
\usepackage{fancyhdr}
\pagestyle{fancy}
\renewcommand\headrulewidth{0pt}
\fancyhf{}
\fancyfoot[R]{\vfootline\hspace{\linepagesep}\thepage}
\newlength\linepagesep
\setlength{\linepagesep}{5pt}
\newcommand*\vfootline{\textcolor{blue}{\rule[-2pt]{1pt}{2\ht\strutbox}}}
\begin{document}
\lipsum
\lipsum
\lipsum
\end{document}

The syntax of \rule is
\rule[<vertical shift>]{<width of the rule>}{<height of the rule>}
If the rule should go down you could use eg.
\rule[-\ht\strutbox]{1pt}{2\ht\strutbox}

Remark: You are using a KOMA-Script class. So it is recommended to use package scrlayer-scrpage instead fancyhdr:
\documentclass[12pt, a4paper,twoside,footheight=23pt]{scrreprt}
\usepackage{blindtext}% only for dummy text
\usepackage{xcolor}
\usepackage{scrlayer-scrpage}% sets pagestyle scrheadings automatically
\clearpairofpagestyles
\rofoot*{\vfootline\hspace{\linepagesep}\pagemark}
\lefoot*{\pagemark\hspace{5pt}\vfootline}% for twosided document
\newlength\linepagesep
\setlength{\linepagesep}{5pt}
\newcommand*\vfootline{\textcolor{blue}{\rule[-2pt]{1pt}{2\ht\strutbox}}}
\begin{document}
\blinddocument
\end{document}
Other example:
\documentclass[12pt, a4paper,footlines=2]{scrreprt}
\usepackage{lipsum}% only for dummy text
\usepackage{xcolor}
\definecolor{ultramarineblue}{rgb}{0.25, 0.4, 0.96}
\renewcommand\chaptermarkformat{\chaptername\ \thechapter\autodot\ \ }
\usepackage[automark,headsepline,markcase=upper]{scrlayer-scrpage}
\clearpairofpagestyles
\ohead{\leftmark}
\rofoot*{\vfootline\hspace{\linepagesep}\pagemark}
\lefoot*{\pagemark\hspace{5pt}\vfootline}% for twosided document
\addtokomafont{headsepline}{\color{ultramarineblue}}
\newlength\linepagesep
\setlength{\linepagesep}{5pt}
\newcommand*\vfootline{{\usekomafont{headsepline}\rule[-2pt]{1pt}{2\ht\strutbox}}}
\begin{document}
\chapter{CTitle}
\lipsum
\section{STitle}
\lipsum
\end{document}

Note that the star in \rofoot* and \lefoot* ensures that page style plain will use the same contents as page style scrheadings. By default chapter pages get page style plain.
fancyhdrmy first suggestion would not use this package. Butfancyhdrbreaks some KOMA-Script features. Eg. optionsheadsepline,footseplineetc. does not have an affect and you can not use\addtokomafontor\setkomafontto change the font of page header and footer etc. So it is recommended to use the KOMA-Script packagescrlayer-scrpagewhile it is still possible to usefancyhdr. – esdd Feb 05 '18 at 12:53