"The meeting between the teams of negotiators ended near midnight," a spokeswoman for Israeli Justice Minister Tzipi Livni, Israel's chief negotiator, said in a Twitter message.
"Both parties described the meeting as a long and serious one and were determined to continue the talks soon," Mia Bengel said.
The nearly 5-hour talks in Jerusalem Wednesday night were held at a secret location.
"No photo opp. No statements. Why? To allow the teams to work together, and not think about the media waiting outside," Bengel said on Twitter.
The next round of talks is expected to be held next week, also under a media blackout, in Jericho in the West Bank.
Livni, a proponent of establishing a Palestinian state alongside Israel, met with Palestinian Authority chief negotiator Saeb Erekat, who negotiated the 1993 Oslo Accords with Israel.
U.S. special envoy for Israeli-Palestinian negotiations Martin Indyk did not initially take part in the discussions, The Jerusalem Post said. He met instead with Israeli Prime Minister Binyamin Netanyahu, three days after meeting with Palestinian Authority President Mahmoud Abbas.
A Western diplomat told British newspaper The Guardian the "atmosphere" surrounding the talks was "not positive."
"This is politically very tough," the diplomat said.
They also came almost 24 hours after Israel freed 26 long-serving Palestinian prisoners, many convicted of deadly attacks on Israelis.
And they came a day after Israeli media reported the Israeli Interior Ministry gave final approval to 890 new apartments in contested East Jerusalem. Two days before, the Israeli Housing Ministry said it approved construction of 1,200 apartments in other parts of Jerusalem and the occupied West Bank.
The peace talks had been stalled for three years, in large part over Israel's continually increasing settlements and Palestinian concerns about their repercussions on the viability of a future Palestinian state.
Most members of the international community regard the Israeli settlements as illegal under international law. U.S. Secretary of State John Kerry, who intensive shuttle diplomacy brought the Middle East negotiators together, called Israeli settlements "illegitimate" Tuesday.
State Department spokeswoman Jen Psaki wouldn't explain the distinction between "illegal" and "illegitimate" Wednesday. She added it was the Israeli and Palestinian negotiators' place, and not Washington's, to determine the legitimacy or illegitimacy of any Israeli settlements.
"We oppose any unilateral action," Psaki said, and "we have concerns about ongoing continued settlement activity."
Ban's two-day visit was intended as a symbolic show of support for the first direct talks between the two sides since Israeli Prime Minister Ehud Olmert and Abbas met in 2008.
Ban was first to meet with Abbas and other senior Palestinian officials in the West Bank city of Ramallah, the Palestinian Authority's administrative capital.
Ban will also lay a wreath at the grave of slain Israeli Prime Minister Yitzhak Rabin, the Post said.
Rabin was key in the signing of the Oslo Accords, which created the Palestinian Authority and granted it partial control over parts of the Gaza Strip and West Bank.
After signing the accords with Palestine Liberation Organization Chairman Yasser Arafat, Rabin said, "We who have fought against you, the Palestinians, we say to you today, in a loud and a clear voice, enough of blood and tears ... enough!"
Rabin was assassinated in 1995 by a religious Zionist who said he opposed Rabin's peace initiative, particularly the Oslo Accords.
Ban is expected to end his visit Friday with dinner with Indyk and U.S. Ambassador to Israel Daniel Shapiro.