I think you do understand "at bay." It does mean something like "in the background" or "under control." The point here is that Tom needs to not get complacent, not feel like he has already succeeded even though he is picturing himself getting safely into his apartment.
In lots of things that people do, they need to really concentrate. They need to not think "oh, I've got this, I've made it" and then lose their concentration and fail. You can see this in people playing sports, you can see it in people getting in car crashes when they think that they're near to home and everything is safe for sure. Tom has to avoid that.
If Tom doesn't keep concentrating with all his might on getting back in, if he relaxes because he has it made, he might still fall and die. That's why he has to control those feelings.
Having retrieved the yellow sheet which represents weeks of work, Tom Benecke loses his balance and knocks into the open window which, "shuddering," closes on him. When he is unable to open it, he very carefully draws back his right hand, and strikes the glass with the heel of his palm. Unfortunately, his arm "rebounded" from the pane of glass, causing him to totter, and he realizes he cannot strike the glass any harder without falling. In "the security and relief of his new position" he ponders his situation, disbelief that a single pane of glass can prevent him from reentering his apartment. Tom decides that once in his apartment, he will give release to his feelings, run across the room, jump on the floor, etc. But, now his desire for this is too strong and "astonishingly intense" and he must keep this feeling "at bay" while he conserves energy and concentrates upon how he will break the glass. He then tries various methods, to no avail. This is the moment of truth for Tom, for he cannot wait for Clare and must do something before his grip weakens.