Friday's deaths bring the total number of Palestinians killed at the Gaza border to 124 since protests there began on March 30, including 60 people killed in a single day last month.
Israel Defense Forces had issued warnings on leaflets throughout Gaza and on Twitter, warning civilians to stay away from the fence.
He said that the protests against Israel - which also call for an end to grinding Israeli and Egyptian blockades on Gaza - would continue, despite scores being killed.
There have been no Israeli casualties from the more than two months of confrontations but farmland on the Israeli side has been damaged by fire from the kites and balloons.
A press vest did not protect an AFP photographer from Israeli bullets fired during protests in Gaza.
Although the stadium that was slated to host the match is in west Jerusalem, Mr Rajoub had complained that it is in a neighbourhood built on the site of a former Palestinian village destroyed during the war surrounding Israel's creation in 1948.
Rajoub has long urged Fifa to expel Israel from the global football federation, citing Israeli travel restrictions on Palestinian footballers and because Israel maintains teams in West Bank settlements.
"They organize this, Hamas".
Around 2 million people live in Gaza, a lot of them the stateless descendants of refugees from what is now Israel. -AFP Youths carry tires on their shoulders as they head to join other protesters gathered along the border fence with Israel.
Her statement came a day after Argentina's national soccer team cancelled a friendly match in Jerusalem over pressure and physical threats from pro-Palestinian groups. Both have received political and financial support from Iran, but they also pursue their own agendas.
The Jewish state maintains a crippling blockade of Gaza it says is necessary to isolate Hamas.
Several European countries have tried to dissuade Palestinians and Arab countries from demanding a vote in the General Assembly after last week's U.S. veto.
Al-Quds day was observed throughout the country on Friday. Israel captured east Jerusalem in the 1967 Mideast war and annexed the area in a move that is not internationally recognised. Israel's current government has said it will not accept a partition of the city as part of a peace deal with the Palestinians. The compound sits on the ruins of biblical temples and is revered by Jews as the holiest site of their religion.
Thousands of protesters assembled on the streets of Tehran to hear their leaders trash Israel, the U.S., and their allies across the globe, with many chanting "Death to America" while burning the United States flag.
In Iraq, thousands of Iran-backed Shiite militiamen in uniform marched through the streets of the capital of Baghdad on Friday, setting an Israeli flag on fire and carrying posters of the late Iranian leader Ayatollah Ruhollah Khomeini and Supreme Ayatollah Ali Khamenei.