You forgot join's first argument.

#!/usr/bin/perl

my $declon = -88.9999999999999999999;
my $declat = 44.1111111111111111111;

print($declon, "\n");  # -89
print($declat, "\n");  # 44.1111111111111

my @lon = split(/\./, $declon);
my @lat = split(/\./, $declat);

$lon[1] = substr($lon[1], 0, 6);
$lat[1] = substr($lat[1], 0, 6);

my $lat = join('.', @lat);
my $lon = join('.', @lon);

print "$lat\n";
print "$lon";
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Again, I removed the useless quotes around $declon and $declat.

As you can see by the two prints I added near the top, -88.9999999999999999999 gets stringified as -89. You're going beyond the precision of a double. This also demonstrates where your algorithm fails. (-89 prints as "-89." instead of "-89.000000".) What you want is

# Round (.5 rounds up)
$num = int($num * 1000000 + 0.5) / 1000000;
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or maybe

# Truncate towards 0.
$num = int($num * 1000000) / 1000000;
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You can also do it using string manipluation for a little bit more precision:

$lon = sprintf('%.6f', $declon);
$lat = sprintf('%.6f', $declat);
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Example 1:

#!/usr/bin/perl

use strict;
use warnings;

my $declon = -88.9999999999999999999;
my $declat = 44.1111111111111111111;

my $lon = int($declon * 1000000 + 0.5) / 1000000;
my $lat = int($declat * 1000000 + 0.5) / 1000000;

printf("%.6f\n", $lon);  # -88.999999
printf("%.6f\n", $lat);  # 44.111111
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Example 2:

#!/usr/bin/perl

use strict;
use warnings;

my $declon = -88.9999999999999999999;
my $declat = 44.1111111111111111111;

printf("$declon\n");   # -89
printf("$declat\n");   # 44.1111111111111

printf("%.6f\n", $declon);   # -89.000000
printf("%.6f\n", $declat);   # 44.111111
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