Younis Mahmood fired visiting Al Wakra into a sixth-minute lead but Majidi levelled three minutes later before adding his second after 24 minutes.
The win lifts Al Gharafa into sixth place, now just one place and one point behind Al Wakra.
In the day's other game, Umm Salal climbed out of the relegation zone with a 3-0 win over bottom side Al Ahly.
All the goals came after the break, with Magno Alves (68, 80) and Everaldo Cabore (77) on target.
Umm Salal are now out of the bottom two, a point clear of Al Khrityat, while Al Ahly are five points from safety.