The Scot believes he would have found it tough to keep the pair if former Old Trafford boss Sir Alex Ferguson had come calling for them during his time at Goodison Park
The Premier League champions had an initial £28 million (€32.6m) joint bid for the midfielder and left-back rejected, and then described as "derisory and insulting" by the Toffees.
However, United have made an improved offer of £35m (€40.8m) for the pair, and Moyes believes it will be difficult for Roberto Martinez to prevent Fellaini and Baines from leaving Goodison Park.
"I definitely do [sympathise with Roberto Martinez]," Moyes told reporters. "But I also know that if I was the Everton manager and Sir Alex [Ferguson] had come asking for Baines and Fellaini, I would have found it very difficult to keep them.
"I always felt the right thing to do was what was right for the players. All we can do is our job here.
"Roberto is in a new job and I am sure he will get to understand how Everton work. I know exactly how Everton work. I signed every player at Everton.
"I respect Everton greatly and I don’t want to do anything that would in turn affect them. Of course, taking their players would affect them but I am certainly only doing what I have to do in my job."
Moyes spent 11 years in charge at Goodison, after joining from Preston North End in 2002.