Place the \caption{abc} command in the heading ended by \endfirsthead and use a \caption[]{...} in the repeated heading. the [] form suppresses the writing to the toc file. (See the longtable documentation).
As @lockstep noted datatool hides this longtable feature, so you need to unhide it:-)
\begin{filecontents*}{dt4.csv}
40,120,40
40,90,60
35,180,20
55,190,40
40,120,40
40,90,60
35,180,20
55,190,40
40,120,40
40,90,60
35,180,20
55,190,40
40,120,40
40,90,60
35,180,20
55,190,40
\end{filecontents*}
\documentclass{article}
\usepackage{longtable,datatool}
\textheight=12\baselineskip
\makeatletter
\def\DT@capfix{\@dtl@contcap}
\def\LT@c@ption#1[#2]#3{%
\LT@makecaption#1\fnum@table{#3}%
\def\@tempa{#2}%
\ifx\@tempa\DT@capfix\let\@tempa\@empty\fi
\ifx\@tempa\@empty\else
{\let\\\space
\addcontentsline{lot}{table}{\protect\numberline{\thetable}{#2}}}%
\fi}
\makeatother
\begin{document}
\listoftables
\DTLloaddb[noheader,%
keys={Temperature,Time,DT4},%
headers={\shortstack{Incubation\\Temperature},%
\shortstack{Incubation\\Time},\shortstack{Time to\\Growth}}%
]{dt4}{dt4.csv}
Now display the data in a table:
\DTLdisplaylongdb[
caption=ho hum,
shortcaption=fi fo,
contcaption=hoo ha
]{dt4}
\end{document}
