When you make pag-ibig you involve feelings, LOVE, passion. When you have sex you just have sex, without ipinapakita your feelings for the person, with no affection, with no sweet words or whatever, that's just sex.
Well both are pretty much the same. Making pag-ibig can be also be halik and caressing other than intercourse and it also can be others like oral sex and anal sex (especially for mga tomboy and homosexuals).