Rory Hie of Cerritos won the event with a 66. Murrieta Valley's Rickie Fowler, who won the tournament last year with a 64, shot a 68 to place second.
Tom Whitney from La Quinta finished third with a 69 after winning a playoff.
The top 28 individuals qualified for the CIF/Southern Section Golf Assn. Final, which will be held June 1 at The SCGA Golf Course in Murrieta.
La Ca"ada assistant coach Rich Wheeler said Lee, who led the Spartans to the Rio Hondo League championship before winning the league's individual championship, had a strong long game. But Lee couldn't convert on some of his putts, Wheeler said.
La Ca"ada Coach Richard Tetu said he was surprised that Lee didn't advance.
"I thought Abe would go to the end," Tetu said. "Statistically, he was our best player.
"The level of golf at the high school level is really improving."
Crescenta Valley Coach John Pehar said Ward, who played a key role in leading the Falcons to their second consecutive Pacific League championship, started out his round with bogeys on the 14th and 15th holes before recording a triple bogey on the 17th hole.
Pehar said Ward, who missed the first month of the season because of a broken left arm, was frustrated because he couldn't generate any momentum on the difficult course.
"The wind was a little bit of a factor," Pehar said. "He felt like he didn't get any breaks.
"I told him that he got to play with the big-time players and that not too many people get to do that. I think he'll come back and play better next year and he now knows the course layout."