Mike Zunino was 0-for-17 before getting two hits and driving in two runs. The Mariners, who scored two runs in the first, have won 11 of their last 14.
"We had the lead early, which is big for me, for my pitching, because I'm all about pitching to contact," Iwakuma said through an interpreter.
Iwakuma (12-6) was masterful while allowing four hits and no walks. Since July 1, the right-hander is 7-2 with a 1.63 ERA, 65 strikeouts and four walks in 72 innings over 10 starts.
"He was outstanding," Mariners manager Lloyd McClendon said. "He commanded all of his pitches. He was in and out, up and down. Did a tremendous job for us."
The Phillies, who have scored three runs or less 65 times this season, got just one batter to second base against Iwakuma. They have lost six of their last eight.
The Mariners needed three pitchers in the ninth to preserve the victory. The last of the trio, Fernando Rodney, came on with two outs and the tying run at the plate and struck out Cody Asche to record his 36th save in 39 opportunities.
"We have a strong belief in our bullpen, so I was able to watch the TV very calmly," Iwakuma said.
Asked if he was tempted to let Iwakuma come out for the ninth, McClendon said, "No, no."
The Phillies avoided their 14th shutout when Chase Utley scored on Yoervis Medina's wild pitch. Domonic Brown followed with an RBI double to pull Philadelphia within 5-2 before Medina hit Carlos Ruiz to put runners on first and second for Asche.
A.J. Burnett (6-14) lost his fifth straight decision and dropped to 0-6 with a 6.41 ERA in seven starts since the All-Star break. He allowed six hits with four walks and hit two batters in 7 2/3 innings.
Mariners: RF Michael Saunders, who has been on the DL since July 11 with a strained left oblique, made his 10th rehab start Tuesday night for Triple-A Tacoma. Entering Tuesday, he was batting .258 at Tacoma.
Phillies: OF John Mayberry Jr. played in his first rehab game with Triple-A Lehigh Valley at Pawtucket on Tuesday night. Mayberry has been on the DL since July 21 with left wrist inflammation.
Mariners: LHP James Paxton (3-0, 2.20) makes his sixth start of the season when the teams wrap up their three-game series on Wednesday afternoon. The 25-year-old is unbeaten in nine career starts, with his latest victory last Friday at Detroit when he allowed one run on five hits in six innings. Paxton will be facing the Phillies for the first time.
Phillies: LHP Cole Hamels (6-6, 2.44) will look for some better luck. He has a 1.71 ERA in his last three starts but is 0-1 over that stretch due to a lack of run support that has plagued him all season.
Burnett signed a one-year deal with a player option for next year in the offseason. After Tuesday's outing, he sounded as if he might decline the option.
Asked if he would return to the Phillies in 2015, Burnett said, "Probably not. We'll see."
Philadelphia's Ben Revere went without a hit for just the second time in his last nine games, going 0-for-4 with a rare strikeout. Revere entered Tuesday second in the NL in batting at .313 and leading the league in hardest to fan (one strikeout per 11.9 plate appearances).
Copyright by STATS LLC and The Associated Press
PHILADELPHIA, PA - AUGUST 19: Starter A.J. Burnett #34 of the Philadelphia Phillies delivers a pitch in the...
31,592 (72.4% full) - % is based on regular season capacity
82 degrees, cloudy
Home Plate - Kerwin Danley, First Base - Ron Kulpa, Second Base - Mark Ripperger, Third Base - Lance Barksdale
Marlon Byrd has slugged .480 this season in at-bats to end on a pitch in the lower third of the zone or below, eighth highest among qualifiers. Hisashi Iwakuma has thrown the third-highest percentage of pitches in that zone this season among qualifiers (57 percent).