The margin was 64% against with 36% in favour, despite a recommendation for acceptance from IMPACT union officials. There was a turnout of 100%.
Last week, management at the airline warned that if the deal was rejected it would institute up to 1,100 compulsory redundancies and scale back services.
IMPACT said that statement had angered many Aer Lingus staff.
Earlier today, pilots accepted the programme by a margin of 81% to 19%. The turnout was over 80%.
Under the programme, there would be a 15% cut in the number of pilots and a 10% pay cut.
Increments would be frozen for three years and there would be reductions in pension benefits and increases in productivity.
The President of the Irish Airline Pilots' Association, Captain Evan Cullen, said that by backing the cost-saving measures, pilots had once again demonstrated their massive commitment to Aer Lingus.
Mr Cullen said they had already incurred considerable losses to date by investing large amounts of their own money in shares in the airline.
He said the cost savings agreed with management, along with those given over recent years, represented another investment by IALPA's members.
Aer Lingus said it would comment on the outcome of the ballots when all the results were known.
