Pennington connected on a 39-yard scoring pass to Ted Ginn Jr. in the first quarter and Williams sprinted 51 yards for a score in the second.
Williams accumulated 105 rushing yards for the Dolphins (5-4), who have won three straight contests.
Ronnie Brown ran 16 yards for the other Miami score.
The Seahawks (2-7) scored on a 35-yard pass interception run by Justin Babineaux, field goals of 36 and 27 yards by Olindo Mare and a 3-yard pass from Seneca Wallace to John Carlson.
Seattle has lost five of its last six games.