The American Conference's second win in a row gave them a 23-22 edge in the all-time rivalry when the conference format has been used to select elite squads.
Derek Carr, who completed 11-of-15 passes for 114 yards, connected with Walker on an 18-yard touchdown pass with 91 seconds remaining and Chris Boswell's conversion kick gave the American Conference a 24-23 lead.
Walker also caught a 4-yard touchdown pass from Alex Smith on the first American Conference march of the second half in a rainstorm.
"It made it very difficult," Walker said. "It's hard to catch the ball when it's raining. But that's our job."
Jared Goff tried to rally the National Conference but Denver defender Von Miller forced a fumble and recovered it to end the final threat.
"That's my job. I've got to rush," Miller said. "That's where I make my money, whether it's Denver or Orlando."
Each player on the winning team took $64,000, twice what those on the losing team received.
Drew Brees flipped an 8-yard touchdown pass to Adam Thielen to cap the game's opening drive and put the National Conference ahead 7-0.
Americans kicker Chris Boswell booted a 41-yard field goal and Graham Gano responded from 43 for the Nationals.
Harrison Smith, a Minnesota Vikings linebacker, returned an interception of a Ben Roethlisberger 79 yards for a touchdown to boost the National Conference lead to 17-3.
Smith guided the Americans near the goal line before a Patrick Peterson pickoff ended the march and a 40-yard Gano field goal put the Nationals ahead 20-3 at half-time.
Smith's touchdown toss to Walker pulled the Americans closer and Carr's 39-yard pass to T.Y. Hilton set up LeSean McCoy's 2-yard touchdown run that lifted the Americans within 20-17 late in the third quarter.
Gano split the uprights from 38 yards for his third field goal to boost the lead to 23-17 and Peterson intercepted Carr to shut down another American Conference drive with 8:46 remaining.
But the Nationals surrendered the ball on downs in their own half of the field to give the Americans possession, setting up the go-ahead scoring drive.