The move has been made possible after the FA agreed a £6m compensation package over five years with Division Three clubs. The chairmen of the 72 League clubs gave the proposal their support at the Chairman's Conference on Friday, before rubber-stamping the plans at the AGM on Saturday morning.
The chairmen were heavily criticised for rejecting the move last summer. But 12 months of negotiations with the FA over a cash settlement have changed their minds and two clubs will now be relegated into the Conference in May 2003.
Under the terms of the FA deal, all 24 Division Three clubs will receive £50,000 every August for the next five years. The two promoted teams will win a £35,000 hand-out, with relegated sides receiving parachute payments.
Lincoln City chairman Rob Bradley's club finished 22nd in Division Three this season. He said: "I know two down would have troubled us this year, but the principle is right".
"There are three or four teams going up and down in the other divisions, and I think there should be freedom of movement through the football pyramid".
"To have one team going up is not fair. You've got to stick with your principles, no matter how nervous you might be".
"Cambridge chairman Roger Hunt agreed that fear of relegation was not a good enough reason to keep the system as it is".
"I've always been in favour." he said.
"If you have three-up and three-down between Division One and the Premiership, you can't have restrictive practices at the bottom".
"We're all frightened of being relegated, but two-up, two-down is the right thing for the good of football".
Had the rules been in operation this year Conference champions Boston would have been joined in the League by second-placed Dagenham and Redbridge. Bottom-of-the-League Halifax would have been joined in the Conference by Bristol Rovers, who ended the season in 23rd place in Division Three.