Wanderers saw their eight-match unbeaten run halted by an 88th-minute strike from Carlos Edwards at Portman Road, leaving them five points adrift of the play-off places with eight matches remaining.
But Pratley remains optimistic of clinching a top-six finish in the Championship with an important game at Charlton now looming after the international break.
He told the Bolton News: "We are disappointed the run we have been on has come to an end, but we have to dust ourselves down.
"We have been on a great run so we won't be too down on ourselves.
"It is all good when things are going well for everyone to be smiling and patting each other on the back.
"This has given us another little wake-up call. Maybe that is what we needed with this chance of getting into the play-offs we have got.
"Hopefully, we can get the right response and win our next game at Charlton.
"After a defeat you always want to play as quick as possible. It is two weeks to the next game so it is a bit of a shame in that respect but we will be ready."