Goals from Nene and Lisandro Lopez had the hosts two goals up within four minutes and Nicolas Flores added a third in the 18th minute, soon after Al Saeed Mohammed had pulled one back.
Othmane El Assas reduced the deficit further from the penalty spot just after the hour mark, but any hopes of a comeback were swiftly quashed as Meshal Mubarak netted Al Gharafa's fourth goal and then Nene completed his treble with a 79th-minute strike and an 88th-minute penalty.
Elsewhere, sixth-placed Al Wakra fought from two goals down to draw 2-2 at home to Al Khor. Julio Peu's first-half brace had looked to have set the visitors on their way to victory, but Anouar Diba halved the deficit on the stroke of half-time and then salvaged a point with a 55th-minute penalty.
Finally, Al Khrityat battled from behind to win 2-1 at second-bottom Muaither, Yahia Kebe (29) and Jaycee Okwunwanne (66) the men on target after Fozil Musayev's 14th-minute opener.