You can do it with basically the same form as the sed command you gave using standard perl stuff, like so:

open INF, '<', $IFName or die $!;
open OUF, '>', $OFName or die $!;
while (my $line = <INF>) {
     ... do stuff ...
     print OUF $new_line;
}
close INF or die $!;
close OUF or die $!;

rename($IFName, $IFName . ".bak") or die $!;
rename($OFName, $IFName) or die $!;
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Above is off the top of my head, and is therefore untested...