Just disambiguate the $1 with braces as well: ${1}:
#!/usr/bin/perl
use strict;
use warnings;
my @lines = split /\n/, <<'END';
begin{verbatim}
hello all
end{verbatim}
END
s{((?:begin|end)){verbatim}}{${1}{whatever}} for @lines;
print "$_\n" for @lines;
__END__
begin{whatever}
hello all
end{whatever}
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