On 4 December 1988, Hernâni scored a rare goal, netting for Benfica in a 2–0 home win against former side Setúbal. A fortnight later, after a 2–0 home success against Lisbon neighbours Sporting Clube de Portugal, he tested positive for cocaine, and received a three-month ban. He was a first-team regular in the latter part of the 1989–90 campaign, and played the whole of the 1990 European Cup Final, lost 1–0 to A.C. Milan; he remained with the club for a further four years, but made only six appearances combined.