Lynch compiled 42 yards on 20 carries, becoming the Seahawks' first 1,000-yard-plus rusher since Shaun Alexander in 2005.
Seattle (7-7) won its third straight with the help of Tarvaris Jackson, who completed 19-of-31 passes for 227 yards with a touchdown.
The Bears, meanwhile, lost their fourth in a row, falling to 7-7 as Caleb Hanie was limited to 111 yards on 10-of-23 passing. He hurled a TD pass but was picked off three times in the defeat.
Chicago lost wide receiver Johnny Knox to a back injury after taking a hard hit in the first quarter.