mysql> show variables like "%timeout%";
+----------------------------+-------+
| Variable_name              | Value |
+----------------------------+-------+
| connect_timeout            | 10    |
| delayed_insert_timeout     | 300   |
| innodb_lock_wait_timeout   | 50    |
| innodb_rollback_on_timeout | OFF   |
| interactive_timeout        | 28800 |
| net_read_timeout           | 30    |
| net_write_timeout          | 60    |
| slave_net_timeout          | 3600  |
| table_lock_wait_timeout    | 50    |
| wait_timeout               | 28800 |
+----------------------------+-------+

Без рестартиране на MySQL:
SET interactive_timeout=60;
SET GLOBAL interactive_timeout=60;

Рестартиране на MySQL:

/etc/mysql/my.cnf

[mysqld]
…
interactive_timeout=60
wait_timeout=60
…