However, he fought back to win 3-6 6-0 6-1 and book his place the third round of the Miami Masters.
"It was very different without him, it's been a hard few days," Murray told Sky Sports News. "He's been a big part of my career and to not have him around is going to be tough, but I just need to get on with it now and try to get back to playing my best tennis."
On his victory over Ebden, Murray added: "He was playing well at the net in the first set. I had six break points, I think, but I couldn't convert.
"I played better in the second and third sets. I got broken right at the beginning of the third set, I played a sloppy game and needed to fire myself up, but I turned it around after that and won six games in a row."
Murray will face Spain's Feliciano Lopez in round three.