Maloof, a senior at St. Francis, shot a nine-over par 80 to finish tied for 41st. Bouchard, a sophomore at Flintridge Prep, carded an 83 to tie for 57th.
The top 30, including ties, advanced to the CIF Individual Final, which will be held Monday at Industry Hills Golf Club's Babe Zaharias Course. The cut was 77.
Jonathan Sanders of New Community Jewish fired a 70 to earn medalist honors.
Things looked good for Maloof, who finished third in the Mission League, before he encountered trouble during his last three holes. Maloof, a standout football player with the Golden Knights, posted two double-bogeys in a row and completed it with a bogey.
"I just couldn't finish and the greens were hard and fast," Maloof said. "I hit the ball great and I was two-over-par through 14.
"I missed some putts in the middle and toward the end. I'm happy with my season, but I wish I qualified [for the final]."
Bouchard, who placed second in the Prep League for the second straight season, said he had some quality tee shots that put him in good position for a par or birdie.
However, Bouchard, making his second appearance in the event, couldn't overcome some trouble elsewhere.
"I came into the round having worked on some things and I felt good with my practices," Bouchard said. "I hit a lot of solid shots and my putting was OK considering the greens.
"I just had some bad bunker shots and I had a triple-bogey on the sixth hole. It was a fun experience. I wish I could have played better."
Jay Lin of La Cañada had a 74 to tie for eighth and Burroughs' Kelsey Danzeisen notched a 76 to tie for 20th. Both qualified for the CIF final.
Noah Bernstein of La Cañada finished with an 83 to tie for 57th. La Canada's Derek Patao had an 86 to tie for 75th, while teammate Joshua Suh tied for 88th with a 92.