The rookie outfielder came up short, finishing third behind St. Louis' David Freese and Atlanta's Michael Bourn, in the voting that completed Thursday afternoon.
Instead, he'll spend the time off back home in Las Vegas, something both he and the Nats are looking forward to.
"I just want to thank all the fans that went out and voted for me and everything the Nationals did and everybody else in the entire world that voted for me every day," Harper said after the Nationals' 6-5 win Thursday. "But hopefully in the next couple years I can get in there. I'm excited to get back home for a couple days and just calm down for a little bit."
It was the fourth consecutive year the Nationals had a Final Vote candidate -- Cristian Guzman in 2009, Ryan Zimmerman in 2010, Michael Morse in 2011 and Harper this year. The team has never had one of its players win the contest.
Harper entered the last day of the voting in second place behind Freese, but fell to third during the final hours, when fans could go to Twitter and use players' respective Final Vote hashtags -- Harper's was #BryceIn12 -- to earn more votes.
Rangers pitcher Yu Darvish is the American League Final Vote winner. The Nationals will still be represented in Kansas City next week by shortstop Ian Desmond and pitchers Stephen Strasburg and Gio Gonzalez, making up the largest contingent of Nationals at an All-Star Game since the franchise moved to Washington in 2005.
Harper, 19, finished the San Francisco series 6-for-14 with five runs and three RBIs.
"He's played great, he's played hard," third baseman Ryan Zimmerman said. "Every day, he comes here ready to work. Even when you are 19 years old, you need a break every now and then. So he can heal up and get some of those bangs and bruises that all of us need some time off to let heal. It's good. I would've liked to see him go [to the All-Star Game] obviously. He's been a real big part of this team and he's fun to watch. It would've been good for the game, but I think Freese is obviously very deserving."
Manager Davey Johnson said, "Good," when he heard Harper would not be heading to Kansas City and is just fine with only Desmond, Strasburg and Gonzalez making the trip.
"He's been not rushed up here, but he's been playing every inning except I gave him a rest for maybe one inning," Johnson said of Harper. "I think he could use the time off to catch his breath rather than having the all-day excitement at the All-Star Game."