Exeter Crown Court heard that the men were working on a new student accommodation scheme for Exeter University at the former Elmfield Nursery in New North Road when the incident happened in February 2008.
Cowlin Construction was fined £85,000 and ordered to pay £20,000 in costs by the court.
Prestoplan Ltd, which provides timber frame buildings, was fined £35,000 and ordered to pay £22,000 towards costs and Somerset Carpenters Ltd, which supplied labour at the site, was fined £50,000 with £20,000 costs.
Somerset Carpenters were served with a prohibition notice by the HSE following an inspection at the site which banned them from working until safety measures had been put in place to stop workers falling down the lift shaft.
A wooden platform was then erected over the shaft but two weeks later this collapsed, sending Ricki Slocombe,35, and Matthew Blackmore, 29, both from Bridgwater, falling to the ground floor.
Blackmore suffered a broken back and Mr Slocombe suffered two broken legs and had to use a wheelchair for several months. He has been unable to return to work since.
Speaking after the hearing, HSE inspector, Simon Chilcott, said: “This was a terrifying incident for the two men which could easily have led to their deaths.
“As it was, they suffered severe injuries, which were life-changing in the case of Mr Slocombe.
“Contractors and employers must make sure they have taken all reasonable measures to provide a safe environment for workers to work in and that any temporary structures are secure.”