The Phillies scored two runs in the ninth on wild pitch by Yoevis Medina and Domonic Brown's RBI double. After Carlos Ruiz was hit by a pitch, bringing the tying run to the plate, closer Fernando Rodney came in.
Rodney ended the game by striking out Cody Ashe.
"It's been a rough year and it's still my job to do what I can do," Burnett said.
Burnett has a player option for next year. When asked if plans to pitch in 2015, he said, "I have no idea. Probably not, but we'll see."
Iwakuma (12-6) is in his third season with the Mariners. He doesn't throw as hard as Burnett but is a craftsman on the mound, changing speeds and most important, throwing strikes.
"He was really a master at mixing pitches and changing speeds," Phillies manager Ryne Sandberg said. "He threw his curve at three different speeds."
Sandberg still has faith in Burnett, but he continues to be plagued by control problems.
"He still has a good breaking pitch and velocity," Sandberg said. "It's just a matter of getting ahead of hitters."
For most of the season Burnett has been pitching with a hernia, but he insists that hasn't caused his problems.
Burnett walked Austin Jackson and Dustin Ackley on eight pitches to start the game. The two executed a double steal and Jackson, who earlier stole second base, scored on Robinson Cano's RBI groundout to second.
After Burnett struck out all-star third baseman Kyle Seager for the second out, Logan Morrison hit an RBI single past second baseman Chase Utley.
Burnett settled down after that.
The Phillies struggled against Iwakuma, but at least they had company.
The rest of MLB hasn't done too well against the 2013 all-star, who missed more than a month to begin the season with a strained tendon in his right middle finger.
Over his previous nine starts, he had a 1.83 ERA, striking out 54 and walking just four in 64 innings.
With the Phillies trailing by 2-0, Ryan Howard just missed hitting a home run with one out in the fourth inning. His shot hit the wall in left-center field, good for a double. On Ryan Howard bobblehead night, no less.
Iwakuma ended the inning by striking out Marlon Byrd and Brown swinging on sinkers.
Seattle went up, 3-0, when Seager drilled a 3-0 Burnett sinker deep to right field for his 19th home run of the season in the sixth inning.
Burnett departed after allowing a two-run single to Mike Zunino with two outs in the eighth inning. He threw 125 pitches, 72 for strikes, while Iwakuma threw 74 of his 96 pitches for strikes.
In 72/3 innings, Burnett allowed six hits and five earned runs, striking out nine but walking four. Burnett's ERA in seven starts since the all-star break is 6.41, continuing a downward spiral.