Previously the four spots open to the regional tournament from Major League Soccer were the MLS Cup champions and runners-up, the US Open Cup winners and the winners of the Supporters Shield for the best regular season record.
The change, requested by US Soccer and MLS, and granted by CONCACAF's executive committee, will see the Cup runners-up lose their spot and instead the champions from both conferences will qualify.
For the 2014/15 competition, Portland Timbers will join Sporting Kansas City (MLS Cup), New York Red Bulls (MLS Supporters Shield) and DC United (Lamar Hunt U.S. Open Cup) as the four representatives from US Soccer.
New York won the Eastern Conference with 59 points, Portland the West with 57.
"Achievement in the MLS regular season is important," Nelson Rodriguez, MLS executive vice president for competition, technical and game operations, said.
"Awarding a spot to the points leader from both conferences is a worthy reward and confers greater importance on regular-season matches."
If a Canadian team grabs one of the four slots, or a single MLS team accounts for more than one berth, the US-based team with the next best regular season record outside the two conference winners would be award the Champions League place.
Canada has one berth awarded to the Canadian Championship winner.
The winners of the CONCACAF Champions League advance to the prestigious FIFA Club World Cup.
CONCACAF is the Confederation of North, Central American and Caribbean Association Football.