Linebacker Bowman went down with a likely torn ACL injury to his left knee while left guard Iupati fractured his left ankle, the team said.
Iupati's injury occurred early in the game on a fourth-down plunge into the end zone by 49ers running back Anthony Dixon.
The 331-pound (150 kg) guard was buried under a pile of players on the goal line and had to be helped off the field.
Bowman's injury in the second half was another devastating blow for the 49ers. He and Iupati both left the locker room after the game on crutches.
Bowman took the ball away from receiver Jermaine Kearse just short of the goal line in a fourth-quarter play, but had his leg bent badly when Kearse fell on him.
Adding insult to injury, the play was not ruled a fumble and Seattle was given the ball on the one-yard line. San Francisco, however, did not suffer on the scoreboard as the Niners stopped them from scoring on fourth down.
"I know how tough he is," linebacker mate Patrick Willis said of his friend. "I could hear him yelling."
"He's going to be all right. He's strong mentally and physically."
The victory sent the Seahawks to the National Football League's February 2 Super Bowl in New Jersey against the Denver Broncos.
(Reporting by Larry Fine in New York, Editing by Julian Linden)
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