I have mentioned it a few times before but IEEE does not directly use your .tex file. It's there to supply the bare minimal so if it looks like an article it's enough. It doesn't have to be following the standards internally.
They will recode your article with their own terrible terrible workflow, rasterize your images and ruin your math after acceptance. I've been using the following for a couple of years without any issues. It uses subcaption and does a superb job even though it has a command clash due to the redefinitions.
\documentclass[final]{ieeetran}
\usepackage{tikz,lipsum}
\usepackage[labelformat=simple]{subcaption}
% Training subcaption package to comply with
% IEEE standards. We can ignore the warning
% generated by caption.sty which is due to
% the redefinition of \@makecaption
\DeclareCaptionLabelSeparator{periodspace}{.\quad}
\captionsetup{font=footnotesize,labelsep=periodspace,singlelinecheck=false}
\captionsetup[sub]{font=footnotesize,singlelinecheck=true}
\renewcommand\thesubfigure{(\alph{subfigure})}
\title{My title}
\author{my author}
\begin{document}
\maketitle
\begin{abstract}
\lipsum*[1]
\end{abstract}
\lipsum[2-5]
\begin{figure}
\begin{subfigure}[b]{.6\linewidth}
\centering%
\begin{tikzpicture}
\draw[help lines] (-1,-1) grid (1,2);
\end{tikzpicture}
\caption{A caption}
\label{fig:a}
\end{subfigure}%
\begin{subfigure}[b]{.4\linewidth}
\centering%
\begin{tikzpicture}
\draw[help lines] (-1,-1) grid (1,2);
\end{tikzpicture}
\caption{B cap}
\label{fig:b}
\end{subfigure}
\caption{Two figures.}\label{fig:1}
\end{figure}
\end{document}

If you only want the caption labels leave the sub \caption{} definitions empty and describe the subfigures in the main caption. If you want to remove also the (a),(b) use \phantomcaption commands as described in the manual.
\caption? You can, even inieeetran. When I add\caption{A caption}to your MWE, I obtainFig 1. A caption. Or is it that you don't want to use\captionbut\subfloatinstead? – Werner May 09 '13 at 16:08captionpackage and the\captioncommand. Of course you can use\captionbut should not use thecaptionpackage since it is incompatible to theIEEEtrandocument class. So better replace\usepackage{subfig}with\usepackage[caption=false]{subfig}to prevent loading thecaptionpackage. – May 09 '13 at 16:09\caption– dustin May 09 '13 at 16:13captionpackage since\usepackage{subfig}does load it unless you say\usepackage[caption=false]{subfig}. The warning you get does not come from LaTeX itself but from thecaptionpackage. – May 09 '13 at 17:34