Monica Wright added 14 points for Minnesota (25-7), which won its seventh straight game.
The two teams will face each other again next week in the best-of-three first-round series since Seattle already had clinched the fourth and final seed.
Moore hit 7 of 10 shots from the field and Whalen 7 of 9. The Lynx pulled away from Seattle with a 23-14 run in the second quarter.
The Lynx beat Seattle in the first round last year. They won the WNBA title in 2011.
Tanisha Wright led Seattle (15-17) with 14 points. Tina Thompson had just five points and shot 2 of 8 from the field.
Minnesota has won 11 of the past 13 games against the Storm, including a 4-0 sweep this year. The Lynx last swept Seattle in a regular-season series in 2001.
Whalen scored 17 and Moore 10 to help the Lynx to a 40-28 halftime lead. Whalen scored four during a 10-0 run late in the second quarter to give the Lynx an 18-point lead. They led by 24 early in the fourth quarter.
Seattle starting point guard Temeka Johnson missed the game with a heel injury and is considered day to day. She averages 10.4 points and four assists per game.
The Lynx beat Seattle 75-60 on Saturday and 97-74 on Aug. 31. Both teams have two regular-season games left.