They deployed on-field spies and applied disciplined pressure to keep Wilson in the pocket.
The San Francisco defense know that Wilson is at his most dangerous whenever he escapes the pocket. Not necessarily as a runner, although his 458 rushing yards are nothing to sneeze at.
But Wilson is absolutely deadly when he throws on the run. His accuracy on the move and ability to manufacture a play when protection fails, is part of the pint-sized passer's growing aura.
But shrewd 49ers defensive coordinator Vic Fangio wasn't about to let Wilson embarrass his tough and resourceful unit. He made sure he always had a free hitter available to track Wilson whenever the quarterback became mobile.
Of course, Fangio made such mobility difficult by designing his pass rush to trap Wilson in the pocket. The two-pronged scheme was brought to life with violent force on the game's opening drive.
The Seahawks faced a 3rd-and-2 and planned a rollout pass designed to get Wilson away from pressure. The 49ers were in their base 3-4 defense and inside linebacker NaVorro Bowman would be the group's spy.
Outside linebackers Aldon Smith and Ahmad Brooks both blitzed, but they each took wide-angled pass-rush lanes. That meant Wilson wasn't given obvious escape routes around either edge.
As he rolled out, Wilson attempted to outrun Brooks and head for the sideline. At the same time, Bowman sped across the field like a thundering Gazelle and soon laid a hit on Wilson a Rhino would have been proud of.
Bowman's awesome sideline-to-sideline quickness is what separates him from most middle linebackers. It makes him a great equaliser against a running quarterback like Wilson.
Later in the first quarter, Fangio employed a different front and that meant a new spy. Wilson faced a 3rd-and-12 at the Seattle 25-yard line and had to convert against the 49ers 4-2-5 nickel front.
Fangio moved Smith over right tackle Breno Giacomini. He let mammoth defensive lineman Justin Smith rush from a wide angle on the other side.
Fangio also shifted Brooks inside to a defensive tackle alignment next to Ray McDonald. The pair were shifted toward the right side of the Seahawks O-line.
This was part of the 49ers plan to clog the side Wilson usually runs to. At the snap, Brooks bailed out into a short zone drop and stood spying Wilson in case he fled the pocket.
With Brooks in his running lane, Wilson had to stay in and attempt a pass against seven-man coverage. His throw fell incomplete and the Seahawks punted.
Even when Wilson was allowed to run, the 49ers made he sure scampered the way they wanted him to go. The best example came in the fourth quarter, with the Seahawks facing 3rd-and-8 at the San Francisco 13.
Aldon Smith lined up over left tackle Russell Okung and took an inside rush move. Dual-threat quarterbacks like Wilson usually seize on inside moves to run from the pocket.
But that's just what the 49ers wanted. They wanted the right-handed quarterback to run to his left, where it would be more difficult for him to throw accurately across his body.
With Brooks maintaining another wide rush lane on the right, Wilson soon took the bait and headed left.
Throwing from a difficult angle, and with 49ers defensive backs clamping on his receivers in man coverage, Wilson's errant pass fluttered to the ground.
The Seahawks had to settle for a field goal which gave them a slender 17-16 lead. That meant the San Francisco offense only needed a field goal to win. Phil Dawson soon kicked the decisive points to give the 49ers a 19-17 victory.
Wilson has been driving defensive coordinators mad with his skills as a runner. But Fangio's crafty unit let him rush just once for a measly two yards.
If these two fierce rivals renew hostilities in the playoffs, Fangio is sure to enlist his disciplined spies to try and keep Wilson in check again.
image: © Neal D