print join("\n",split(/\~/,$var1))."\n";

Rather than concatenating a newline why not place an empty string at the end of the things to be joined.

$ perl -e '
> $var1 = q{abc~123~def};
> print join qq{\n}, split( m{~}, $var1 ), q{};'
abc
123
def
$
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I hope this is of interest.