You can use '+<' to open the file for read and write without truncating. Then seek does work and the print overwrites the beginning of the file.

$ echo -ne "foo\nbar\n" > file
$ cat file
foo
bar
$ perl -le'open my $fh, "+<", "file" or die $!; seek $fh, 0, 0 or die 
+$!; print $fh "bazz";'
$ cat file
bazz
ar
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