Seahawks coach Pete Carroll called timeout with 30 seconds left, but the officials had announced two plays earlier that Seattle used its last one when receiver Doug Baldwin was injured.
After huddling, then meeting with two different people from the sideline, the officials determined the previous stoppage had been on an incomplete pass, so the Seahawks were not charged with a timeout.
Under NFL rules, teams are required to use a timeout for an injured player in the final two minutes, whether the clock is running or not.
"It was my error," referee Bruce Hermansen said in a statement. "We gave them (Seattle) the additional timeout because of the incomplete pass stopping the clock before the injury occurred. When in effect, the clock has no bearing on the play at all, whether it's stopped or running, we should not have given them the additional timeout."
The NFL is using replacement officials while the regular officials are locked out.
In Green Bay, the replacement officials called a total of 18 penalties, some of them questionable and drawing animated complaints from both sidelines.
"Some of the penalties were definitely a little bizarre," Packers quarterback Aaron Rodgers said.
49ers coach Jim Harbaugh was furious with the replacement referee crew early on, after they called Aldon Smith for unsportsmanlike conduct for taking off his helmet after a sack of Rodgers in the first quarter.
Harbaugh seemed to question several other calls, but didn't criticize the crew afterward.
"I don't know what I'm supposed to say or not say," he said.
And in Cleveland, the Eagles converted a fourth-and-1 on the winning drive after QB Michael Vick scrambled for 9 yards and fumbled on third down. He recovered, but Browns coach Pat Shurmur threw his red challenge flag and asked the replacement officials to review the play.
However, referee Ken Roan discussed the play with the booth and announced it was "not challengeable."
"I know it was a fumble," Shurmur said. "I saw us with the ball. So that's why I challenged it."