At its height some 75 firefighters tackled 100ft (30m) high flames, after the blaze broke out at about 14:00 BST.
Black smoke coming from the coal-fired power station led to problems on nearby roads, with drivers and householders advised to keep windows shut.
The blaze at the site near Castleford has now been brought under control.
West Yorkshire Fire and Rescue Service (WYFRS) said no-one was injured but the blaze had resulted in the partial collapse of the tower, believed to be used to remove sulphur dioxide from gases produced at the power station.
National Grid said the station was currently on "summer shutdown" and had not been generating electricity.
It said a major substation on the site was not thought to have been damaged.
Owner SSE said everyone on the site had been accounted for.
The BBC's Matt Richards tweeted to say a number of small explosions had been heard coming from the fire at one stage.
An eyewitness told the BBC: "Well at first we heard the fire siren go off and then we saw a thick black plume of smoke.
"We went outside and then about 10 minutes later it just all went up in a rage. Just a rage of flame."
Ian Bitcon, area manager for WYFRS, said the fire had been ferocious.
He said: "The building has buckled and is around 30ft lower than its sister building because of the fire.
"The company will need to demolish the part of the building affected by the fire, but we are still at the stage where there is enough firefighting that is going on that they cannot start that yet."
He said crews were expected to work through the night damping down the blaze.
The fire caused delays on the M62 and A1(M) for several hours when smoke blew across the road.
The B6136 Stranglands Lane in Knottingley is closed.
Public Health England advised motorists in the area to keep windows and air vents closed and to turn off air-conditioning.
Householders were also told to keep doors and windows closed and stay indoors if possible.
Ferrybridge C is situated on the River Aire and is the third coal-fired power station to be built on the site since 1924.
The power station first fed electricity into the national grid in February 1966.
A fire at Ferrybridge C power station in West Yorkshire has caused the partial collapse of a tower on the site.