I think your code is fine, though it could be made more succinct without sacrificing clarity, and it has a strong "C accent". :-). Here's how I would "perlify" it:

use strict;
use warnings;
my $input    = shift;
my $min      = -180;
my $range    = 360;
my $bin_size = 5;
my $n_bins   = $range/$bin_size;
my @binarray = map [ ( 0 ) x $n_bins ], 1..$n_bins;
  
open my $in, $input or die "Oops! Can't open $input: $!\n";
while ( <$in> ) {
  my @indices = map to_index( $_ ), split;
  $binarray[$indices[ 0 ]][$indices[ 1 ]]++;
}
close $in or die "Failed to close $input: $!\n";

for my $row ( @binarray ) {
  print "$_\n" for @$row;
}

sub to_index {
  return ( $_[ 0 ] - $min )/$bin_size;
}
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