Williams missed three times at 2.31 metres after clearing 2.28 on his third attempt on a wet and cold day in Eugene but clinched his spot on the American team because the third place finisher did not have the "A" qualifying standard.
"The whole goal was to make London and now I am there I want to get on that podium," said Williams.
"These conditions, they were tough. It was really difficult for me to get in a groove and jump to my capabilities," said Williams, whose personal best is 2.37.
"What I did today is really not a reflection of me."
The Eugene resident added: "I definitely need to start jumping in the rain here a little more often."
The seemingly ageless Jamie Nieto won the competition at 2.28 in a reflection of the weather. The 35-year-old did not have a miss before failing three times at 2.31.
"I am so happy," said the former US champion. "In 2008, I missed the Olympic team. I got second and didn't have the 'A' standard."
Collegians Erik Kynard and Nick Ross finished second and third, both at 2.28.
Nieto and Kynard will join Williams in London, but Ross will stay at home because he does not have the required standard.
Only the top three finishers in events at the trials book trips to the Games provided they have the qualifying standard.
"It's bittersweet I didn't make the team," Ross said. "I'll definitely be on that podium again."
Five times national champion Nick Symmonds dominated the men's 800 with front-running Alysia Montano claiming the women's race.
Olympian Symmonds brought cheers from the hometown crowd when he sped home in one minute, 43.92 seconds.
"I want to bring a medal back so badly," said Symmonds, who was eliminated in the semi-finals at the 2008 Games.
"The semis are so unforgivable. ....But once you make the finals it's anyone's race."
Khadevis Robinson, like Nieto aged 35, nipped Duane Solomon by one-hundredth of a second for second place.
Montano, who runs with an artificial flower in her hair, won the women's event in 1:59.08 ahead of Geena Gall and Alice Schmidt.
"The flower in my hair represents strength," Montano said.
"People look at women in sports differently. People say, 'Oh she runs like a girl.' And I just say, 'Why the heck not run like a girl?'"
Former world champion Bernard Lagat easily qualified in the men's 5,000. He trailed Lopez Lomong across the finish line with a time of 13:42.83.
Trials 10,000 winner Galen Rupp also was a qualifier in the other preliminary.
The competition takes a planned two-day break beginning on Tuesday. It resumes on Thursday and concludes on Sunday.
1. Nick Symmonds 1:43.92
2. Khadevis Robinson 1:44.64
3. Duane Solomon 1:44.65
Men's High Jump
1. Jamie Nieto 2.28
2. Erik Kynard 2.28
3. Nick Ross 2.28
Men's Javelin Throw
1. Sam Humphreys 81.86
2. Samuel Crouser 80.80
3. Craig Kinsley 79.92
- - - -
1. Alysia Johnson 1:59.08
2. Geena Gall 1:59.24
3. Alice Schmidt 1:59.46
Women's Triple Jump
1. Amanda Smock 13.94
2. Sheena Gordon 13.83
3. Andrea Geubelle 13.79