[^"]+matches one or more of chars that is not '"'.

$TheLine = 'REFERENCE "z:/bin/JAnalyzer/Justice Analyzer Users Guide.p
+df" "package/Justice Analyzer Users Guide.pdf"';

$TheLine =~ /(\S*)\s+"([^"]+)"\s+"([^"]+)"\s*/; 
print "1 is $1 and 2 is $2 and 3 is $3\n";
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Does this do what you want?