Using .env >= 5.0 (tested on 5.5)

In .env

DB_CONNECTION=mysql
DB_HOST=127.0.0.1
DB_PORT=3306
DB_DATABASE=database1
DB_USERNAME=root
DB_PASSWORD=secret

DB_CONNECTION_SECOND=mysql
DB_HOST_SECOND=127.0.0.1
DB_PORT_SECOND=3306
DB_DATABASE_SECOND=database2
DB_USERNAME_SECOND=root
DB_PASSWORD_SECOND=secret

In config/database.php

'mysql' => [
    'driver'    => env('DB_CONNECTION'),
    'host'      => env('DB_HOST'),
    'port'      => env('DB_PORT'),
    'database'  => env('DB_DATABASE'),
    'username'  => env('DB_USERNAME'),
    'password'  => env('DB_PASSWORD'),
],

'mysql2' => [
    'driver'    => env('DB_CONNECTION_SECOND'),
    'host'      => env('DB_HOST_SECOND'),
    'port'      => env('DB_PORT_SECOND'),
    'database'  => env('DB_DATABASE_SECOND'),
    'username'  => env('DB_USERNAME_SECOND'),
    'password'  => env('DB_PASSWORD_SECOND'),
],

Note: In mysql2 if DB_username and DB_password is same, then you can use env('DB_USERNAME') which is metioned in .env first few lines.

Without .env <5.0

Define Connections

app/config/database.php

return array(

    'default' => 'mysql',

    'connections' => array(

        # Primary/Default database connection
        'mysql' => array(
            'driver'    => 'mysql',
            'host'      => '127.0.0.1',
            'database'  => 'database1',
            'username'  => 'root',
            'password'  => 'secret'
            'charset'   => 'utf8',
            'collation' => 'utf8_unicode_ci',
            'prefix'    => '',
        ),

        # Secondary database connection
        'mysql2' => array(
            'driver'    => 'mysql',
            'host'      => '127.0.0.1',
            'database'  => 'database2',
            'username'  => 'root',
            'password'  => 'secret'
            'charset'   => 'utf8',
            'collation' => 'utf8_unicode_ci',
            'prefix'    => '',
        ),
    ),
);

Schema

To specify which connection to use, simply run the connection() method

Schema::connection('mysql2')->create('some_table', function($table)
{
    $table->increments('id'):
});

Query Builder

$users = DB::connection('mysql2')->select(...);

Eloquent

Set the $connection variable in your model

class SomeModel extends Eloquent {

    protected $connection = 'mysql2';

}

You can also define the connection at runtime via the setConnection method or the on static method:

class SomeController extends BaseController {

    public function someMethod()
    {
        $someModel = new SomeModel;

        $someModel->setConnection('mysql2'); // non-static method

        $something = $someModel->find(1);

        $something = SomeModel::on('mysql2')->find(1); // static method

        return $something;
    }

}

Note Be careful about attempting to build relationships with tables across databases! It is possible to do, but it can come with some caveats and depends on what database and/or database settings you have.

From Laravel Docs

Using Multiple Database Connections

When using multiple connections, you may access each connection via the connection method on the DB facade. The name passed to the connection method should correspond to one of the connections listed in your config/database.php configuration file:

$users = DB::connection('foo')->select(...);

You may also access the raw, underlying PDO instance using the getPdo method on a connection instance:

$pdo = DB::connection()->getPdo();

Useful Links

1. Laravel 5 multiple database connection FROM laracasts.com
2. Connect multiple databases in laravel FROM tutsnare.com
3. Multiple DB Connections in Laravel FROM fideloper.com

MySQL has a different timeout than PHP. You could increase it in php.ini on the line mysql.connect_timeout = 14400. Also increase the default_socket_timeout = 14400

Note that if your PHP setting allow you to do an ini_set, you can also do as follows:

ini_set('mysql.connect_timeout', 14400);
ini_set('default_socket_timeout', 14400);

This gentleman (Olivier) had the same problem! (A year ago) He wrote a small adaptation for the Controllers! It's pretty small and it turns out, it works in 1.3 and 2.x.

Anyhow, this is my final solution, that I put in the app/Model/AppModel.php:

class AppModel extends Model
{
  /**
   * Connects to specified database
   *
   * @param String name of different database to connect with.
   * @param String name of existing datasource
   * @return boolean true on success, false on failure
   * @access public
   */
    public function setDatabase($database, $datasource = 'default')
    {
      $nds = $datasource . '_' . $database;      
      $db  = &ConnectionManager::getDataSource($datasource);

      $db->setConfig(array(
        'name'       => $nds,
        'database'   => $database,
        'persistent' => false
      ));

      if ( $ds = ConnectionManager::create($nds, $db->config) ) {
        $this->useDbConfig  = $nds;
        $this->cacheQueries = false;
        return true;
      }

      return false;
    }
}

And here is how I used it in my app/Controller/CarsController.php:

class CarsController extends AppController
{
  public function index()
  {
    $this->Car->setDatabase('cake_sandbox_client3');

    $cars = $this->Car->find('all');

    $this->set('cars', $cars);
  }

}

I'm betting, I'm not the first or last one with this problem. So I really hope this information will find people & the CakePHP community.