Miller was limited in practice all week by an ankle injury suffered in last week's 29-22 win over the New York Jets and was listed as questionable on Friday's injury before the team downgraded him to out Saturday.
The Texans (10-4) can clinch the AFC South title with a win over the reigning Super Bowl champions on Sunday.
Miller was a huge part of the turnaround by the Texans, who opened the season with three consecutive losses before ripping off nine straight victories to seize control of the division.
In his seventh NFL season overall and third with Houston, Miller is 83 yards shy of reaching the 1,000-yard mark for the third time in his career.
The 5-foot-10, 221-pound Miller rushed for at least 100 yards four times in a six-game span before he was limited to 33 yards and a touchdown on 14 carries in a 24-21 loss to Indianapolis on Dec. 9.
A fourth-round pick of the Miami Dolphins in the 2012 NFL Draft, Miller had only three carries for eight yards before he was injured against the Jets.
Backup Alfred Blue, who has rushed for 473 yards and two touchdowns on 143 carries this season, is expected to get the start against the Eagles.
There is a chance that second-year running back D'Onta Foreman makes his season debut on Sunday. Foreman rushed for 327 yards in 10 games as a rookie in 2017 before suffering a season-ending Achilles tear.
Also listed out for Sunday's game were Texans wide receiver Keke Coutee (hamstring) and nose tackle Brandon Dunn (ankle).