Houston suffered a mild abdominal strain in the Magpies' defeat to Gold Coast last Friday night and will miss the next two weeks.
The former Port Adelaide superboot had scans after playing the Suns, with results ruling him out of facing the Dockers and Richmond.
Hill will sit out a fourth straight match after dealing with personal reasons, and battling with illness last week.
"Hill returned to training over the weekend," Collingwood high performance boss Jarrod Wade said.
"His focus is on resuming full training before a timeline is placed on his return."
Along with Houston, veteran Jeremy Howe will leave another hole in Collingwood's defence after suffering an adductor strain against Gold Coast, ruling him out for two weeks.
But in better news for the Magpies, forward Beau McCreery is set to return against Fremantle after recovering from a hamstring that led him to miss the past three matches.
Premiership star Jordan De Goey is due to come out of concussion protocols in coming days after copping a hit at training.
But De Goey will be put through a two-week training block before being considered to play.
The 29-year-old has been restricted to five games this season, the last coming in round eight against Geelong.
Collingwood being without a number of key players won't worry them.
In round nine, the Magpies travelled to Perth undermanned and managed to secure a 14-point win against Fremantle at Optus Stadium.
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