Members of the Unite and GMB unions walked out from 08:00 GMT to 12:00 GMT.
The Society of Radiographers in England and Northern Ireland also took part in the strike action.
Unions want a recommended 1% pay rise to be implemented for all staff, but the National Health Service said this would cost too much.
The strike action follows a similar walkout last month. Members of several unions in England also took part.
Kevin McAdam of Unite said the government was "reneging on their miserly 1% pay increase recommendation, even though the health trusts had already factored this cost into their budgets".
"Our members cannot and will not sit back and take further cuts to our pay - we have to stand up for the service we provide," he said.
"We are all proud of our NHS and what it stands for, but what we see now is it being damaged deliberately and patient safety compromised in favour of balancing books and making austerity cuts."
Health Minister Jim Wells said he understood that patient safety would not be compromised, but the industrial action was "regrettable".
"I have made known my intention to exercise a degree of restraint over pay, given the financial challenges and the need to prioritise front-line service provision," he said.
"Subject to the necessary approvals, staff will therefore receive either the incremental progression to which they are entitled or a 1% non consolidated pay award if they are at the top of the pay scale.
"Health and social care staff are our greatest asset, and I recognise well their hard work and commitment."
Mr Wells said his department was "keen to work in partnership with trade unions on an affordable pay system".
Ministers in England have awarded NHS staff a 1% increase, but only for those without automatic progression-in-the-job rises.
Designed to reward professional development, these are given to about half of staff and are worth 3% a year on average.
An independent pay review board had said the 1% increase should be across the board.
It was implemented in full in Scotland.
Northern Ireland has yet to make a decision on pay, while Wales did the same as England but did give extra to the lowest paid. Some unions are balloting their Welsh members about action there.
Thousands of NHS workers in Northern Ireland have staged  a four-hour strike over pay.