Try this out and see it works better. The connect method is not documented to accept a DSN in that format.

#!/usr/bin/perl
use strict;
use warnings;
use v5.10;

use DBI;
say "Perl MySQL Connect Demo";

my $db = 'db'; # or whatever it really is
my $server = 'server'; # ditto
my $dsn = "DBI:mysql:database=$db;host=$server";
my $username = "user";
my $password = 'password';

my $dbh = DBI->connect($dsn,$username,$password);
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See also DBD::mysql Class Methods for the full documentation on connect.

Update: You may also need to add in the port.

Update 2: You may need to set some MySQL specific variables in order to get a secure connection working.

...
my $port = 12345; # whatever is should be
my $dsn = "DBI:mysql:database=$db;host=$server;port=$port;
mysql_ssl=1; 
mysql_ssl_client_key=/var/lib/ssl/client-key.pem; 
mysql_ssl_client_cert=/var/lib/ssl/client-cert.pem; 
mysql_ssl_ca_file=/var/lib/ssl/cacert.pem"; # Your paths may vary...
...
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Hi Mr. Muskrat, thank you for your response...it's been really helpful trying to debug what's going on. The thing is...I don't even want to use SSL to connect, as the connection will manage data that is neither relevant nor important (it's one of the tools percona provides to perform some checks over the data, but I tracked the issue to the connection itself rather than the tool, as I was able to reproduce the error creating that simple connection script). I tried specifying mysql_ssl=0 at the dsn, with no luck. I can connect to the server using mysql client without SSL, but couldn't get it to work with perl. Perl version is v5.22.1 built for x86_64-linux-gnu-thread-multi, and we first started having this kind of issues when we moved from Ubuntu 12.04 to Ubunt 16.04 Any Ideas?

http://linux.uits.uconn.edu/2013/04/30/setting-up-mysql-over-tls/

You need first to set the certificate settings in your mysql client settings (systemwide /etc/my.cnf, user in ~/.my.cnf); after that you can add mysql_ssl=1 to the db handle in your perl script.

Hello wthebutcher,

Welcome to the Monastery. I do not know if you problem is resolved so I would like to add something minor.

I would agree with fellow monk Mr. Muskrat on the connect call but also I would use DBI/RaiseError on your connect call to capture any errors to see at least the possible reason of your error.

From the documentation:

The RaiseError attribute can be used to force errors to raise exceptio
+ns rather than simply return error codes in the normal way.
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Sample of code:

#!/usr/bin/perl
use DBI;
use v5.10;
use strict;
use warnings;
use feature 'say';
use Config::Simple;

my %config = ();
my $path = 'conf.ini';

sub mysql_con {
    Config::Simple->import_from("".$path."", \%config)
    or die Config::Simple->error();

    my $dbh = DBI->connect("dbi:mysql::".$config{'MySQL.host'}.":".$co
+nfig{'MySQL.port'}."", 
               "".$config{'MySQL.user'}."",
               "".$config{'MySQL.pass'}."",
               { 'PrintError' => 1, 'RaiseError' => 1 , 'AutoInactiveD
+estroy' => 1 }
    ) or die "Could not connect to ". $config{'MySQL.host'} .": ". $DB
+I::errstr ."\n";

    my $databases = $dbh->do("SHOW DATABASES LIKE '".$config{'MySQL.db
+'}."'")
    or die "Error: " .dbh->errstr. "\n";

    $dbh->disconnect()
    or warn "Error disconnecting: $DBI::errstr\n";

    if ($databases eq 1) {
    return "Database: ". $config{'MySQL.db'} .
        " exists not creating: ". $config{'MySQL.db'} ."";
    }
    return "Database: ". $config{'MySQL.db'} .
    " does not exist create: ". $config{'MySQL.db'} ."";
}

say mysql_con();
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I also use the Config::Simple module as I prefer to when I have multiple scripts connecting to multiple databases. Sample of config file (conf.ini) bellow:

[MySQL]
user=user
pass=password
host=localhost
port=3306
db=PerlMonks
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Update: Adding ssl certification to connect:

#!/usr/bin/perl
use DBI;
use v5.10;
use strict;
use warnings;
use feature 'say';
use Config::Simple;

my %config = ();
my $path = 'conf.ini';

sub mysql_con {
    Config::Simple->import_from("".$path."", \%config)
    or die Config::Simple->error();

    my $dbh = DBI->connect("dbi:mysql::".$config{'MySQL.host'}.":".$co
+nfig{'MySQL.port'}.",
               mysql_ssl=1;
               mysql_ssl_client_key=/etc/mysql/certs/client-key.pem; 
               mysql_ssl_client_cert=/etc/mysql/certs/client-cert.pem;
               mysql_ssl_ca_file=/etc/mysql/certs/ca-cert.pem",
               $config{'MySQL.user'},
               $config{'MySQL.pass'},
               { 'PrintError' => 1, 'RaiseError' => 1 , 'AutoInactiveD
+estroy' => 1 }
    ) or die "Could not connect to ". $config{'MySQL.host'} .": ". $DB
+I::errstr ."\n";

    my $databases = $dbh->do("SHOW DATABASES LIKE '".$config{'MySQL.db
+'}."'")
    or die "Error: " .dbh->errstr. "\n";

    $dbh->disconnect()
    or warn "Error disconnecting: $DBI::errstr\n";

    if ($databases eq 1) {
    return "Database: ". $config{'MySQL.db'} .
        " exists not creating: ". $config{'MySQL.db'} ."";
    }
    return "Database: ". $config{'MySQL.db'} .
    " does not exist create: ". $config{'MySQL.db'} ."";
}

say mysql_con();

__END__

$ perl mysql.pl
Database: PerlMonks exists not creating: PerlMonks
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You can also read more about in similar question with examples DBI:mysql connection over SSL fails

Hope this helps, BR.