Rupp, who also won the 10,000m at the trials, followed his coach's race plan to near perfection and surged past former world champion Lagat in the last five metres to the delight of the crowd at the stadium of his former university.
"Bernard is a great closer, I was just trying to keep pushing," said Rupp of his breakthrough finish against the Kenyan-born Lagat, who holds the American record at the distance.
The 26-year-old had never previously beaten Lagat but with a burst of late energy, the Oregon native hauled in Lagat to win in 13 minutes, 22.67 seconds.
"I feel like the luckiest guy," said Rupp.
The last man to win a 5,000-10,000 double at the US trials was Curtis Stone in 1952.
Rupp, never known for his strong finish, also shattered late American icon Steve Prefontaine's 1972 meet record by 0.13 seconds.
A stern talk by his coach, the former marathon runner Alberto Salazar, and hours of work had inspired the triumph, he said.
"Alberto told me beforehand ... you are going to have to beat people in the last lap, the last 100, in London," Rupp said.
"'You needed to start getting ready for that now.
"If you can't do it here, you may as well forget about London because you are not going to be able to do it there'.
"He was pretty blunt with me, but that is what I love about him," Rupp said of Salazar, who also coaches Britain's 5,000-10,000 Olympic hopeful Mo Farah.
Lagat finished less than a stride behind Rupp in 13:22.82.
Lopez Lomong claimed third in 13:24.47. All three qualify for London.
Rupp had made his first move to the front with about a lap to go only for Lagat to surge ahead coming off the final bend.
"Normally I am the guy who sits back (until the end)," Lagat said, "But I guess I used a little bit more than I normally reserve for the final kick so it was a learning process."
U.S. record holder Brad Walker cleared 5.67 metres to win the pole vault on the crisp, damp day in Eugene.
No one was more ecstatic with their performance, however, than Lance Brooks, who won the men's discus with his final heave of 65.15 metres.
The 28-year-old, who once worked seven concurrent jobs to support himself, would not have had the qualifying standard necessary to make the U.S. squad for London without the throw.
"I knew I had to calm down for the my last throw," said Brooks. "I just had to relax."
Long jumper turned sprinter Tianna Madison cruised through the rain to the day's fastest time as qualifying began in a highly anticipated women's 200m.
Madison, the 2005 world long jump champion, clocked 22.57 seconds to win her heat as she worked to make the U.S. team for London in a second event. She was second in the 100 metres earlier in the trials.
World 100m champion Carmelita Jeter, Sanya Richards-Ross, Allyson Felix and Jeneba Tarmoh were also among those who advanced.
Jeter, the 100m trials winner, sprinted home in 22.63, the second fastest time, to take her heat with Richards-Ross, already on the US team with a win in the 400, clocking 22.67 for third fastest.
Two-times Olympic silver medallist Felix (22.82) and training partner Tarmoh (22.90), the two sprinters involved in a controversial dead heat for third place in the 100m, posted the sixth and eighth fastest qualifying times.
The sprinters must decide by Sunday whether they would like a runoff or a coin flip to break their 100 metres tie.
World champion Christian Taylor easily led qualifying in the men's triple jump, bounding 17.27 metres on his only attempt.
World indoor champion Will Claye was second best at 16.80.
Olympic silver medallist Kerron Clement showed he is still a contender in the 400 hurdles, leading qualifying with a run of 49.37 seconds. Olympic champion Angelo Taylor was second fastest at 49.53.
The trials continue through Sunday with the top three finishers in each event booking tickets provided they have met the Games' qualifying standard.