RevTeX 4.1 caption issues

Indeed the behavior you've described is the default in revtex4-1.

This isn't "in effect", as you said, just because you're loading the caption package, which is incompatible with that class.

So, don't load either caption nor subcaption and you will have your captions in a \small font and justified.

MWE

\documentclass[reprint,aps,prl,twocolumn ,groupedaddress,nobibnotes]{revtex4-1}
\usepackage[demo]{graphicx}

\begin{document}
\begin{figure}
\includegraphics[width=.9\linewidth]{circuits.png}
\caption{This is a long sentence to test whether the caption is justified
 or not. Unfortunately it is not.}
\end{figure}
\end{document} 

Output

---

EDIT (in response to the OP's comment)

minipages are not incompatible with revtex4-1.

Here's an example of how to have two images side by side, in one column and in two columns mode.

\documentclass[reprint,aps,prl,twocolumn ,groupedaddress,nobibnotes]{revtex4-1}
\usepackage[demo]{graphicx}

\usepackage{lipsum}

\begin{document}

\begin{figure}
\begin{minipage}[t]{0.48\linewidth}
\includegraphics[width=.9\linewidth]{circuits.png}
\caption{This is a long sentence to test whether the caption is justified
 or not. Unfortunately it is not.}
\end{minipage}\hfill%
\begin{minipage}[t]{0.48\linewidth}
\includegraphics[width=.9\linewidth]{circuits.png}
\caption{Another figure.}
\end{minipage}%
\end{figure}

\begin{figure*}
\begin{minipage}[t]{0.48\linewidth}
\includegraphics[width=.9\linewidth]{circuits.png}
\caption{This is a long sentence to test whether the caption is justified
 or not. Unfortunately it is not.}
\end{minipage}\hfill%
\begin{minipage}[t]{0.48\linewidth}
\includegraphics[width=.9\linewidth]{circuits.png}
\caption{Another figure.}
\end{minipage}%
\end{figure*}
\end{document} 

Output (two images in the same column)

Output (two images spanning two columns)

I had a similar problem as OP: centered captions in the wrong font size. The problem was my use of the package subfig. The solution is to add the following option:

\usepackage[caption=false]{subfig}

See Caption automatically centered in a REVTeX document.