Management allowances worth up to pound;10,836 will be scrapped and levels four and five of the upper pay scale will be replaced with an excellent teachers' scheme available only in schools which say they can afford it.
Mary Bousted, general secretary of the Association of Teachers and Lecturers, said: "It has been a difficult agreement to reach and no one is saying teachers will be jumping up and down about it."
It comes as a School Teachers' Review Body survey reveals that hours worked by primary heads and teachers have increased since the workforce deal was designed to cut lighten their load.
Classroom unions that signed up to the 2003 deal blame primary heads and governors for the work increase and are threatening industrial and legal action if the situation does not improve.
If the pay deal is accepted by the review body, it will replace management allowances, worth between pound;1,680 and pound;10,836 a year with teaching and learning responsibility payments.
All schools will have to carry out staffing reviews by the end of next year to decide who qualifies for the payments, worth between pound;6,500 and Pounds 11,000 for the head of a large to medium-sized department or between Pounds 2,250 and pound;5,500 for those with lesser responsibilities.
The new system aims to ensure payments are made only for specific responsibilities for teaching and learning and not used to retain staff, reward general good performance or pay for administration.
But teachers receiving allowances for those reasons will not qualify for the new payments unless they negotiate new teaching and learning responsibilities. Their allowances will be wiped out three years after the review.
The National Association of Head Teachers predicted that several thousand teachers would fall into that category. Classroom unions said it was impossible to give a figure.
But if the new system makes its expected savings, some of the 192,000 teachers now receiving allowances will lose out.
The Secondary Heads Association said the new deal gave heads more flexibility over pay.
Steve Sinnott, general secretary of the National Union of Teachers, excluded from the joint pay talks, said the plan was a recipe for "turmoil and uncertainty".
The National Association of School Governors said it had "grave concerns" about the excellent teachers' scheme, which pays teachers up to pound;41,000 and warned it could result in employment tribunals.
Teachers will have to prove excellence through pupil results and help with teacher induction, mentoring, and general staff development.
Around a fifth of teachers on UPS3 are expected to qualify.
The Government has recognised that "some additional funding would be appropriate" for the excellent teachers' scheme, but does not specify how much.