Ironically rain delays have meant that the men's final has been held over until the Monday for the last five tournaments but often the semi-finals have not been completed until the Sunday.
The ATP, which runs the ATP World Tour but not the four Grand Slam events, said in a statement that the USTA had recognised "the incredible physical demands of men's tennis".
"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."
The USTA has said that for the moment the new schedule is for the 2013 event only and that the matter would be reviewed after that.