Members of Unite at Faslane, and Coulport, have taken industrial action in recent weeks against employers Babcock Marine.
The union said the row, involving 800 workers at the two Scottish sites, had now been resolved after a pay offer of 2.7% was accepted.
National officer Ian Waddell said: "Our members at Babcock on the Clyde took strike action for the first time in 42 years to win a decent pay rise and I am pleased that an agreement has now been reached.
"The offer of 2.7% as a consolidated rise is a substantial improvement and has been won through the stance our members have taken. They have remained strong, united and dignified throughout and I hope that we can now work with Babcock in an atmosphere of respect for our members."
Workers ranging from hotel and catering staff to those handling nuclear weapons, staged a two hour strike last month and have banned overtime.