Miller's blow from an innocent Stuart Carswell challenge came as the Saints' inability to convert their early chances ended in a Fir Park defeat for Lomas' men.
The frustrated manager said: "It looks like Gary Miller has broken his ankle. We are desperately disappointed for the boy. It's a big blow.
"I think it was just an honest challenge between two players and Gary has come off worst and the shout is he might have broken his ankle."
The Sunday clash ended in controversy as Lomas felt his team should have been awarded a penalty in the 89th minute when Nigel Hasselbaink forced his way through on goal.
"The frustration is that the boys feel it should have been a penalty, I don't know who it was had two arms around Nigel's waist when he broke through at the end and the keeper has made a save," he said.
"There was a bit of a wrestle for the ball but it's quite clear the Motherwell player has two arms round Nigel's waist and that, for me, hampers his shot. He is trying to break free.
"All credit to the goalkeeper, he has come on and had to pick two balls out the net before he had a touch. That could have hit his confidence but he has come up with a good save and got his team the points."
Lomas, who lost Murray Davidson to an ankle injury before the game, felt his team deserved more.
"We didn't really have a defensive midfielder. It was quite an attack-minded set-up so we knew it would be quite an open game," he said.
"Motherwell like to attack. We knew it was going to be who took their chances and unfortunately their conversion rate has probably been better.
"Unfortunately the difference is Michael Higdon, they were three good goals from his point of view and probably not so good from our point of view.
"But I'm proud of the boys for not giving up and making a game of it."