Kubiak's statement came hours after a league source confirmed to NFL.com senior writer Steve Wyche that Williams would miss the season.
"I feel so bad for Mario, because he's such a heck of a player," Kubiak said Monday. "He had really taken to the position he's playing. He was improving every day in practice, improving in every game. I'd never seen him so upbeat about what was going on."
Williams is Houston's all-time sacks leader (53). He set the team's single-season sacks record with 14 in 2007, and he was named a Pro Bowl starter in 2009 and '10.
"I'm disappointed for Mario," Kubiak said. "Obviously, it's tough on the team. We're missing a great player."
Rookie Brooks Reed, a second-round pick, will move into Williams' spot in the starting lineup. Reed had four tackles in about 50 plays in Sunday's game.
"It's a great opportunity here in his young career to step up and be a starter," Kubiak said. "That's why we drafted him. (He's) very capable of doing it. He'll get his opportunity here."
Kubiak said the Texans might bring linebacker Jesse Nading off the practice squad to add depth. Kubiak will meet with general manager Rick Smith and owner Bob McNair to discuss other possible roster moves.
Notes: Kubiak said Andre Johnson, who had hamstring surgery last week, was ahead of schedule in his recovery, but the coach was non-committal on the receiver returning Sunday against the Baltimore Ravens. ... QB Matt Schaub has a sore throwing shoulder and a thigh bruise from Sunday, and FB James Casey left the game with a strained pectoral muscle. Kubiak said both players are "day to day." ... Mike Brisiel left the game with injuries to his ankle and knee, and Kubiak said the guard will be re-evaluated Wednesday. ... LB Brian Cushing had "five or six" stitches to fix a gash on his nose against the Raiders, Wyche reported. The injury didn't cause Cushing to leave the game.
The Associated Press contributed to this report.