Abbas arrived on Wednesday in Madrid from France as part of a tour that will take him to Washington for talks with President George Bush.
Abbas also met King Juan Carlos.
Spanish and Palestinian officials were not immediately available to comment on the 30-minute meeting between Zapatero and Abbas.
The two leaders had been expected to discuss Israel's suspension of contacts with the Palestinian Authority after two drive-by shootings.
The two leaders were also expected to talk about Palestinian legislative elections scheduled for January and a summit next month in Barcelona of European Union heads of state or governments and leaders of countries on the Mediterranean's southern rim.
Abbas and Israeli leaders have been invited to attend the summit.
When they meet on Thursday, Bush was expected to push Abbas to do more to halt anti-Israel violence, battle corruption and build the Palestinian economy.
Abbas, who stopped in Jordan, Egypt, France and Spain on his way to Washington, hoped to win EU and US support for a resumption of peace talks under the roadmap.
He was expected to raise the Rafah crossing issue, and resist US pressure to exclude the radical Hamas movement from participating in the Palestinian legislative elections in January, according to Palestinian foreign minister Nasser al-Qidwa.