Abdullah "stressed the importance of intensifying efforts to create real political prospects for progress toward resolving the conflict", the report said.
Israeli police say an investigation into the deaths is being conducted.
During the talks, the King also highlighted the significance of working with the USA administration to advance the peace process and relaunch serious and effective negotiations between Palestine and Israel based on the two-state solution.
Over the past decades, the Israeli regime has tried to change the demographic makeup of al-Quds by constructing illegal settlements, destroying historical sites and expelling the local Palestinian population.
"The future of the Palestinian issue is at stake and reaching a solution is becoming more hard".
Over the past several months, Abbas, as head of the Palestinian Authority, has stepped up pressure on Hamas, cutting off salaries for civil servants in Gaza, limiting payments to Israel for electricity imports and some medicines.
Abbas suspended security ties with Israel over the crisis. He said that Jordan was "infuriated" by the matter, calling it "unacceptable and provocative behavior". Israeli authorities are investigating the shootings in which a bystander, Bashar al-Hamarneh, was killed.
Jordan's king flew by helicopter to the West Bank in a rare visit seen as a signal to Israel that he is closing ranks with the Palestinians on key issues, such as a contested Jerusalem shrine.
The monarch's visit comes amid growing Jordanian-Israeli tensions over the Jerusalem shrine, the third holiest site of Islam and the most sacred one in Judaism. The new Israeli measures, which Israel eventually reversed, prompted the Waqf Islamic Trust, a Jordanian government body that administers the site, to announce a boycott that devolved into daily clashes between Palestinians and Israeli forces.
Abbas reportedly praised Abdullah for his efforts to defuse the recent Temple Mount crisis.
According to Palestinian Foreign Minister Riyad al-Malki, the Monday meeting resulted in the construction of a joint Palestinian-Jordanian team that will be assigned to deal with future crises and seek to improve joint coordination following the latest Temple Mount flare-up. "It's sending a message 'we are the protectors of al-Aksa, we are united and we are putting you on notice'".