Search for 'Defending a lead', a few threads on that. I tend to have a ready-made tactic to switch to if I know it's going to be a close thing, drop you advanced players back, replace your tricky wingers. Reduce forward runs so your full backs don't run out of position and drop a deep defensive line. Also, try to stuff defence/midfield with tall players, I tend to sub off my short wingbacks for a more beefy centre back who can play on the wings as it saves you a lot of balls over the top if they can head them straight out.
Beyond that, get a squad with good concentration, stamina and natural fitness; and don't overdo the closing down settings for midfield or use 'hassle opponents' all match, it's a sure way to get yourself battered at the end.
Lastly, don't feel ashamed at using defensive tactics, I like to play as Barca and I found it a little odd I couldn't just boss the entire game in the opponent's half, but ultimately Barca have some poor strength players who can get kicked about a bit if you arn't careful. Mix up strength with trickery, don't overdo the flair players who are great at home against **** opposition but no good against the top sides when they don't have the ball at their feet. Those guys are the first who get to sit on the bench when I sub on a DM or two, especially in cup games.
Playing with the tempo and timewasting helps, just don't force a tired team to play a high tempo game, let them knock it around and let the opponents do the chasing, tire themselves out, then hit them late instead of them doing it to you
