Natfhe and the Association of University Teachers, which both represent members in further and higher education, backed their leaders in approving the merger into a new University and Colleges Union.
Among Natfhe members, more than 95 per cent voted in favour, while at the AUT the approval rate was lower, at 79 per cent. Just over a third of members voted.
The new union will have 116,000 members when the merger is formalised in June, with former Natfhe members making up nearly 60 per cent of the total.
Paul Mackney, who was first elected general secretary of Natfhe on a pro-merger platform in 1997, said this was the fulfilment of one of his most important ambitions for the union. He said: "The first thing it will do is get more members. People who were not sure who to join or couldn't understand why there were two unions, particularly in higher education, they will join, I think."
A single union will also put a stronger case to employers, avoiding divisions such as in 2003, when the AUT narrowly voted for a strike while Natfhe narrowly rejected one.
"That wasn't a reason to avoid a merger, it was the best reason to have one," Mr Mackney said.
Both unions are merging from a position of strength, he said, with sound finances and growing membership.
Natfhe's membership rose by 13 per cent (8,000 members) this year, which Mr Mackney attributed to the prospect of a single, stronger union.
Their experience of dealing with the fallout from poorly-handled college mergers would also show them how not to manage the merger, he said.
Further education will become a minority in the new union, with about 40 per cent of the membership being from colleges.
But Mr Mackney said college lecturers' interests would be protected by maintaining separate budgets within the union.
Sally Hunt, general secretary of the AUT, said: "The new union will be a potent force for change in further and higher education. No longer will universities and colleges be able to divide our members over their pay and conditions. The outside world will not be able to ignore the views of those who work in HE and FE when deciding on future policy for both sectors."
Both she and Mr Mackney are expected to seek election as general secretary of the new union after a transitional period of a year.