Mr Benaissa said he wanted to try and restore normal diplomatic ties between the two countries.
However, their four-hour talks ended without any agreement to return their respective ambassadors to Rabat and Madrid.
Despite this, Ms Palacio was quoted as saying that she was very satisfied with the meeting and that the important thing for her was that it took place.
The BBC's Claire Marshall says that the only move forward appears to be the idea of setting working groups to debate some of the obstacles to improving ties.
Thorny issues
Morocco's complaints with Spain are not limited to Perejil.
The most important is over the former Spanish colony in Western Sahara which Morocco controls.
Rabat believes that Madrid favours the territory's independence movement - the Polisario Front - and is blocking the UN from approving Morocco's claim to sovereignty.
Then there are the Spanish north African enclaves - Ceuta and Melilla and various islands including Perejil which Morocco regards as occupied territory.
In addition, Spain also wants to prospect for oil in the waters between Morocco's Atlantic coast and the Spanish Canary Islands.
For its part, Madrid complains that Morocco does not do enough to stem illegal immigration and drug trafficking into Spain.
It also blames Rabat for the collapse of the European Union agreement that allowed Spain to fish in Morocco's rich waters.
But experts say it is in both countries interest to improve relations.
Spain is the second biggest market for Morocco's exports after France and its second biggest investor.