As discussed in the documentation(1):

• After syncdb, execute an ALTER TABLE statement to convert tables

  ALTER TABLE <tablename> ENGINE=INNODB;
  

• or, change settings to use the init_command option for MySQLdb:

  # settings.py
  DATABASES = {
      'default': {
           'OPTIONS': {
               # works because South changes table creation
               'init_command': 'SET storage_engine=INNODB',
           }
      }
  }
  

• or, use post_syncdb trick listed in wiki:AlterModelOnSyncDB,
• or, create a management.py file along with your app, with:

  # management.py
  from django.db import connection
  # syncdb does "import_module('.management', app_name)"
  # IOW, this gets executed before creating the tables.
  connection.cursor().execute('SET storage_engine=InnoDB;')
  

• or, if you use South(2) for migrations, with:

  # settings.py
  DATABASES = {
      'default': {
          'STORAGE_ENGINE': 'INNODB'
      }
  }
  

• or, if you can, edit my.cnf

  # my.cnf
  default-storage-engine=InnoDB
  

• (1) ​https://docs.djangoproject.com/en/dev/ref/databases/#creating-your-tables
• (2) ​http://south.aeracode.org/docs/settings.html#mysql-storage-engine