Israel deployed thousands of police and set up road blocks across Jerusalem on Friday, Micky Rosenfeld, a police spokesman said.
Police also limited Palestinian access to al-Aqsa mosque due to fears violence could break out in the Old City as both Jews and Muslims gathered for prayers.
The Israeli military, for its part, sealed off the occupied West Bank until Saturday night.
The seminary assault was the bloodiest attack on Israelis in two years and the first such in four years in Jerusalem.
"The time for us has come to understand that an external struggle as well as an internal struggle are raging," Rabbi Yaakov Shapira told mourners outside Merkaz Harav seminary.
Shapira, who runs the well-known centre for Jewish studies linked to those leading the Jewish settler movement in the occupied West Bank, called for "stronger leadership" in Israel.
The seminary serves some 400 high school students and young Israeli soldiers, many of whom carry arms.
As Israel buried the victims of Thursday's assault, its military kept up the pressure on Palestinian fighters.
Two of them were wounded, including one seriously, late on Friday in an Israeli strike in the Gaza Strip, local medical sources and witnesses said.
The two members of Izz al-Din al-Qassam Brigades, the armed wing of Hamas, were injured after Israeli forces fired at them east of Gaza City, the sources said.
An Israeli army spokeswoman told the AFP news agency that ground forces fired a missile at a "group of armed men approaching the security fence near Nahal Oz" on the border with Gaza.
Earlier, Israeli defence officials said the perpetrator of Thursday's seminary assault came from east Jerusalem, the predominantly Arab section of the city which Israel captured and occupied in the 1967 Middle East war.