I was running into this problem as well. The db user that WP is connecting as has full schema privileges. To see what problem the application is running in to run the following against your database.
SELECT * FROM wp_yoast_migrations;
In my case I was getting the following error.
Reason: Percona-XtraDB-Cluster prohibits use of DML command on a table (wordpress.wp_yoast_migrations) without an explicit primary key with pxc_strict_mode = ENFORCING or MASTER
My database runs on a Galera cluster with Percona. Temporarily changing pxc_strict_mode to PERMISSIVE, let Yoast upgrade itself, and then et it back to ENFORCING.
See https://www.percona.com/doc/percona-xtradb-cluster/LATEST/features/pxc-strict-mode.html for more information
