Do you have shell access to the server? If so, you can likely upload the file to it (via FTP or rsync), and then use the MySQL CLI tools to import. Or, if you have remote access to the MySQL server enabled for your IP, you can import directly through your local CLI tool.
Here's an example of what I would do regularly:
mysql -u user -p your_magento_db -h server.com < database.sql
rsync -avPz ./database.sql firstname.lastname@example.org:/path/to/temp/location/
mysql -u user -p your_magento_db < /path/to/temp/location/database.sql
The first example requires that you have remote access allowed to your MySQL server, and also the CLI tools installed locally on your machine.
The second example is used when you need to push the database up to the remote server, then you log into it and use the CLI tool there to make the import.
Note that the above command syntax might change depending on your environment, but this is generally the best way to avoid large transfer limits over HTTP.