Ferguson's side were on course for their first draw in 15 league games when Stephen Dobbie struck the winner in added time.
Peterborough had defended stoutly for much of the second half, and Ferguson said: "Unfortunately we didn't quite see it through.
"Brighton were a bit relentless in the second half, we didn't keep the ball well enough and unfortunately we lost it at the end."
Peterborough now host top-of-the-table Crystal Palace on Saturday, and Ferguson added: "We have no time to feel sorry for ourselves.
"If we play like we have in our last two home games then we will have a good chance against a team that has gone top.
"Ian Holloway has a similar philosophy to me. He likes to get the ball out and pass it and it will be a good game for us.
"Home form is paramount for us doing well and they are the kind of performances we need.
"It'll be tough but if we get a display similar to the ones against Derby and Huddersfield we will give Palace a difficult game."