Miller limped off in the closing moments of the Fir Park clash just as Saints saw their late comeback hopes foiled by a crucial save by Motherwell's substitute goalkeeper Lee Hollis.
However, Lomas felt his team should have been awarded a penalty in the 89th-minute incident when substitute Nigel Hasselbaink forced his way through on goal.
Saints had fallen three behind to Michael Higdon's clinical hat-trick and his own side's inability to convert their early chances added to a painful day, which was rounded off when Miller was hurt in an innocuous challenge with Stuart Carswell.
Lomas 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."
Higdon netted twice in the opening 20 minutes and added another instant finish in the 69th minute.
But Saints had enjoyed most of the pressure and they were back in touching distance 10 minutes later through excellent strikes from Hasselbaink and Liam Craig, within three minutes of Hollis coming on after Darren Randolph was taken off with a hamstring problem.
Hollis had little chance with the goals and he rescued the points when he came out to save from Hasselbaink after the Dutchman had forced his way beyond the Motherwell defence.
But Lomas said: "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.
"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."