The Prison Officers’ Association (POA) said staff returned to their posts from 1pm, with those taking part in the industrial action being docked half a day’s pay.
At least 5,000 prison officers across England and Wales were expected to take part in the protests, which began at 7am, over safety improvements in jails and a reduction in violence and overcrowding.
The dispute led to judicial proceedings being abandoned because defendants were unable to arrive at courts. It was unclear if court cases would resume after the strike was called off.
Judge Jeremy Richardson QC, Honorary Recorder of Sheffield, expressed his “displeasure” after making a decision to adjourn the sentencing of a drug gang at Sheffield Crown Court.
He said at least two of the six defendants who were in custody failed to arrive at the court and added he had been told a van waiting to transport at least one of them was stuck outside HMP Manchester.
The sentencing of two teenagers and a youth at Luton Crown Court over a knife fight in a shopping centre was also adjourned on Friday because one of the defendants could not be transported.
Earlier, prison officers involved in the strike action were warned they were acting illegally.
The governor of HMP Bedford, Helen Clayton-Hoar, issued letters to officers, giving them a “direct order to return to work”.
Steve Gillan, general secretary of the POA, said there was a “rising epidemic” of violence and drug taking in prisons.
He told Sky News: “We can’t just keep turning a blind eye to the broken limbs, the smashed eye sockets and broken jaws of our members. They’re people as well.
“Everybody has a right to go to work not in fear for their health and safety.”
The POA said there had been 116 assaults on staff at HMP Bedford in the last six months and some workers had suffered post-traumatic stress disorder due to violent and drug-fuelled conditions.
Brian Cooper, POA branch chairman, said injuries suffered by staff included an officer who had his head stamped on and required surgery for a bleed on the brain and another who had a fractured eye socket who might lose the ability to move his eye properly.
On Thursday, chief inspector of prisons Peter Clarke warned that inmates at HMP Bedford had effectively taken control at the violent, overcrowded and vermin-infested jail.
He issued an urgent notification, which means the government has to publish a response and plan of action for the jail within 28 days.
It is the fourth jail to be subject to the urgent notification process after Nottingham, Exeter and Birmingham.
Prisons minister Rory Stewart, who has pledged to resign if his campaign to tackle drugs and violence in jails is a failure, branded the union “irresponsible” and said the protests were illegal.
He said: “Prison officers do vital and important work and we urge them to return to their duty stations, in line with their obligations to the law and the prison service.”