Fourth-ranked Colorado won the team battle with 90 points, followed by No. 1 Wisconsin with 94 and No. 2 Arkansas with 202.
Boit and Matt Gonzales of New Mexico, both unbeaten this season entering the 10,000-meter race, ran side by side at the front much of the way, but Simon Bairu of Wisconsin surged in the stretch to win in 30:37.7.
Bairu, surprised to win, waved both hands to the crowd of around 6,000.
Boit was in second place until Gonzales passed him in the final 10 meters. Gonzales clocked 30:40.9 and Boit 30:41.8.
Jason Sandford, 20th in 31:26 and Marc Rodriguez, 25th in 31:33.9, joined Boit as All-America performers for Arkansas. It was Sandford's fourth cross country All-America award, matching what only Joe Falcon had achieved for Arkansas.
UA coach John McDonnell, thwarted in his bid for a 40th national title and 12th in cross country, said, "If someone had said before the season we would finish third, I'd have taken it. But I thought as it went on that we had a shot to win."
Shawn Forrest, a UA freshman from Melbourne, Australia, was hurting early in the race and did well to labor home 67th in the team scoring in 32:30.
"Shawn had an off day, but he kept trying," McDonnell said.
McDonnell had hoped that junior miler Said Ahmed could place in the top 30, but Ahmed dropped out after 2,000 meters.
"That was devastating," McDonnell said. "We needed Ahmed to be our fifth man, because Matt Gunn and Adam Perkins were not capable yet."
Gunn was 101st in 32:59, Perkins 149th in 33:29.
"We're a track program," McDonnel said. "We have sprinters, javelin throwers, pole vaulters, and we have 12 1/2 scholarships. Colorado and Wisconsin can give most of their scholarships to distance runners.
"But we'll be good in cross country next year, I promise you. We'll give another scholarship or two to distance runners."
Boit, who picked dry places on the soggy course to surge, said, "I felt OK at 5K, but the last 2K was really tough for me. I gave it all I had, but Bairu ran away from me. Then I thought for the last 200 meters I would finish second, but Gonzales came out of nowhere."
McDonnell said Boit didn't look behind him, because he hadn't had to do that all season.
"He had won so easily that before this race I had to ask him, 'Can you sprint?'" McDonnell said. "But he had an outstanding first year in our program, and he has a great future."
Sandfort put every ounce of energy into finishing 14th among those in the team scoring.
"It was the end of my cross country career, so I gave it everything I had," Sandfort said. "I feel blessed to be on this team. We didn't win, but we came together well and had a good time. I'm glad to be back on the podium with our team.
"I was glad to improve again, and glad Mark got All-American as well. I have an indoor and an outdoor season left and we're going to have a great track team."
Boit said Monday's conditions were the toughest he'd faced this season. His arms and legs were caked with mud at the finish.
"It was perfect weather, but there was no stability with footing," Boit said.
Rain had not been forecast for Monday, but it rained much of the morning, ending about an hour before the race.
"It was a hard course to coach on," McDonnell said. "Fences inside the course made it hard to communicate with the runners."
Brent Vaughn led Colorado in 30:49. Colorado's fourth and fifth runners narrowly edged Wisconsin's fourth and fifth men, providing the winning margin.
Gonzales said, "It was mushy and muddy for all of us. Every time I came up on Boit, he surged. I didn't want to do that the whole race. When he and Bairu broke away, I think they thought I was out of the picture. I knew what I was doing, but I waited a little too late to catch Bairu."
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