EJ Manuel, who has a sprained LCL in his left knee, is doubtful for the game after being limited in practice this week.
"[His knee] did not progress the way that I wanted it to. I give him credit. He's disappointed. He did everything he could when he was out there," Marrone said. "At the end of the day, the decision process was injury-related, meaning that he was not able to do the things at 100 percent that in my opinion we need to do to win this game."
Lewis started in place of Manuel in Sunday's win over the Miami Dolphins. Marrone previously said that he was "110 percent confident" that Manuel would return for the season finale and the team would not consider "shutting down" Manuel for the remainder of the regular season.
"At the end of the day, I made a decision not to put [Manuel] out there for no other reason because I thought Thad would give us the best chance to win this game with EJ's injury not progressing," Marrone said Friday.
Lewis has a 2-2 record as the starter this season. His completion percentage (60.2), passer rating (77.8) and yards per pass attempt (6.6) are all higher than Manuel's numbers.
"It's not just about the mobility, but at quarterback you got to be able to run aspects [of the offense]," Lewis said. "In this instance, sometimes you have to keep guys honest with the zone-read and things of that nature. So I guess, speaking like that, I was probably the best choice."
While Marrone did not rule out Manuel being active for Sunday's game, Friday's decision effectively ends an up-and-down season for the first-round pick. His 42.3 QBR and 77.7 passer rating each rank 30th in the NFL.
Manuel will work this offseason to improve his durability after suffering three knee injuries since August.
"We know it's an LCL. It's a nonsurgical procedure," Marrone said. "We have a plan for after the season to obviously strengthen both of those knees, to build the muscles around the LCL. Obviously the risk factor will become low, even though an LCL injury is one of the lowest-risk injuries in football."
The Bills also ruled out wide receiver Stevie Johnson for Sunday's game. Johnson's mother died Dec. 14, and Johnson remained in California for her funeral Friday.