Next year's men's singles final will be played on Monday allowing the players to have a day's rest after the semi-finals which have traditionally been played on "Super Saturday" along with the women's singles final.
The 2013 women's singles final will take place on Sunday with the semi-finals also on Friday - ending 30 years of the Super Saturday - although no decision has yet been taken on whether the change will be a permanent one.
"By modifying the schedule to allow a rest day between the semi-finals and the final, the US Open has recognised the incredible physical demands of men's tennis," a statement from the ATP said on Monday.
"However, the ATP and its players have made it clear to the US Open that we do not support a Monday final.
"We strongly believe the US Open should keep a similar schedule to the other Grand Slams, with the men's semi-finals completed by Friday and the final on Sunday.
"It is unfortunate the US Open response did not reflect our views on this issue and the ATP and its players will continue to pursue this matter in its discussions with the USTA."
Bad weather has wrought havoc with the US Open schedule in recent years with the men's final, including this year's epic between Andy Murray and Novak Djokovic, being pushed back to Monday for the past five years.
The ATP also gave a lukewarm response to the USTA's announcement of a $4 million rise in prize money for the tournament to a record $29.5 million.
"The prize money increase announced by the US Open for 2013 is appreciated and, together with the 2012 increase, represents the largest increase by the US Open since the ATP Tour began in 1990," it said.
"However, over the last nine months the ATP and its players have asked that the US Open fully recognise the fundamental role of the players in driving US Open revenues, which are the largest in our sport.
"The ATP therefore remains committed to continuing discussions on this issue, with the objective of ensuring that the players' share of the revenues at the US Open truly reflects the value that they generate for the event."
Players have complained about prize money for years, saying purses for the four Grand Slams were too small in relation to the revenue they brought in and too lop-sided in favour of the top competitors who regularly advance to the later stages.
The matter came to a head before this year's Australian Open although talk of a possible strike never came to fruition.