The 49ers' third starting quarterback this year connected with George Kittle in the end zone twice, while Christian McCaffrey ran in San Francisco's other scoring effort.
San Francisco looked the better team from the outset, taking a 14-3 lead into half-time before extending their advantage in the third quarter.
A late field goal and touchdown from Seattle kept things interesting, but ultimately was not enough to keep San Francisco from securing their first division title since 2019.
Purdy finished with 217 yards to go along with his two touchdowns, while Seattle quarterback Geno Smith posted 238 yards and a touchdown in the loss.