The loss ends the season for Burroughs (9-3-3), which finished second in the Pacific League. The Warriors (12-7-3) were runners-up in the Mountview League.
"We just couldn't get into any type of rhythm," Burroughs Coach Allen Machuca said. "It was hard for us to get anything going."
La Puente didn't waste much time getting its first goal, as Leo Villagrana made a nice pass to Oscar Villa who promptly knocked in a header from 10 years out.
The Warriors added to their lead in the 18th after Burroughs goalkeeper John Castro made a fine save. However, the ball bounced back in front of the goal to a waiting David Ramirez, who powered a shot past Castro.
The Indians were able to generate few scoring chances in the first half, which ended with La Puente holding a 2-0 lead.
Burroughs looked inspired at the beginning of the second half. However, it was the Warriors who struck again just four minutes into the half, as Villa tallied his second goal of the match.
"That third goal to start the second half is what really killed us," Machuca said. "That was the dagger."
Burroughs wasn't able to convert on a penalty kick in the 76th minute.
It looked as if Burroughs was going to be shutout as the final seconds of the match ticked off. But the Indians didn't give up, and in the final minute, Joan Alvaraz finally hit pay dirt for the host's lone goal.
"Our boys left it all on the field," Machuca said. "They were out there fighting until the end."