The problem with what you have is that regexes are greedy by default, so that .* is going to eat up every character up to the last > on the line. To prevent this, you can use the ? modifier after the * quantifier:

s/(<body\s.*?>)/$1$newContent/is
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Another problem with your original regex is that it would miss a tag that spanned more than one line. Fixing this problem is the purpose of the /s modifier above.

But parsing HTML with regexes is unwise. Try something like HTML::Parser.