It is permissible to break words at a maqaf. My copy of the BHS does, anyway.
This does not happen automatically with xetex, but you can achieve this by specifying a hyphenation character with fontspec:
\documentclass{article}
\usepackage{polyglossia}
\setmainlanguage{hebrew}
\setmainfont{SBL BibLit}[Script=Hebrew,Contextuals=Alternate]
\newfontfamily\hebhyphen{SBL BibLit}[Script=Hebrew,Contextuals=Alternate,HyphenChar=־]
\begin{document}
\begin{minipage}{5.5cm}
וַיֹּ֣אמֶר אֱלֹהִ֗ים יִקָּו֨וּ הַמַּ֜יִם מִתַּ֤חַת הַשָּׁמַ֨יִם֙ אֶל־מָקֹ֣ום אֶחָ֔ד וְתֵרָאֶ֖ה הַיַּבָּשָׁ֑ה וַֽיְהִי־כֵֽן׃
\hebhyphen
וַיֹּ֣אמֶר אֱלֹהִ֗ים יִקָּו֨וּ הַמַּ֜יִם מִתַּ֤חַת הַשָּׁמַ֨יִם֙ אֶל־מָקֹ֣ום אֶחָ֔ד וְתֵרָאֶ֖ה הַיַּבָּשָׁ֑ה וַֽיְהִי־כֵֽן׃
\end{minipage}
\end{document}

For completeness, here's how you could do it in lualatex.
\documentclass{article}
\usepackage[nil,bidi=basic-r]{babel}
\babelprovide[he,main]{hebrew}
\babelfont[hebrew]{rm}[Contextuals=Alternate]{SBL BibLit}
\exhyphenchar=`\־
\begin{document}
\begin{minipage}{5.5cm}
וַיֹּ֣אמֶר אֱלֹהִ֗ים יִקָּו֨וּ הַמַּ֜יִם מִתַּ֤חַת הַשָּׁמַ֨יִם֙ אֶל־מָקֹ֣ום אֶחָ֔ד וְתֵרָאֶ֖ה הַיַּבָּשָׁ֑ה וַֽיְהִי־כֵֽן׃
\end{minipage}
\end{document}