Ban decided that last year`s list would remain unchanged, but said he was "deeply alarmed" by the "grave violations suffered by children as a result of Israeli military operations in 2014".
"The unprecedented and unacceptable scale of the impact on children in 2014 raises grave concerns about Israel`s compliance with international humanitarian law, notably the principles of distinction, proportionality and precaution in attack, and respect for international human rights law, particularly in relation to excessive use of force," he said.
The UN chief cited a "dramatic increase" in the number of children killed in Israel and in the Palestinian territories in 2014.
At least 561 children (557 Palestinian, four Israeli) were killed and 4,271 injured (4,249 Palestinian and 22 Israeli) last year.
Ban also criticised "Palestinian armed groups" for indiscriminate rocket fire that endangered children in Israel and Gaza.
UN special envoy for children and armed conflict, Leila Zerrougui, had included Israel`s army and Hamas in a draft of the report she had sent to the secretary-general, who had final say on the blacklist.
The list is an annex of a thematic report on children and armed conflict submitted annually to the Security Council.
UN spokesman Stephane Dujarric stressed that "the report is more than the list" and lays out concerns about the plight of children in the Israeli-Palestinian conflict.
Israeli Ambassador Ron Prosor welcomed the decision not to include Israel on the list. The AFP news agency quoted him as saying Ban "was right not to submit to the dictates of the terrorist organisations and the Arab states, in his decision not to include Israel in this shameful list, together with organisations like ISIS, al-Qaeda and the Taliban".
The current list has 51 groups including Boko Haram and the Islamic State of Iraq and the Levant group as well as the armed forces from eight countries such as Syria, Yemen, the Democratic Republic of Congo and South Sudan.
"Ban`s disappointing decision to override the advice of his special representative by removing Israel and Hamas is a blow to UN efforts to better protect children in armed conflict," said Philippe Bolopion, a representative of Human Rights Watch.
"Facts and consistency dictated that both be included on the list, but political pressure seems to have prevailed."
The blacklist of children`s rights violators was released just two months after a UN inquiry found that the Israeli military was responsible for seven attacks on UN schools in Gaza that were used as shelters during the 2014 war.
The board of inquiry confirmed that UN officials working with Palestinian refugees sent twice-daily communications to the Israeli military with precise GPS coordinates of the schools being used as emergency shelters.
The UN is discussing measures to address the findings of the UN inquiry and it remains an open question as to whether they could be used in a possible war crimes case against Israel.
The 50-day conflict in Gaza last year killed 539 children and injured 2,956, most of whom are Palestinians now struggling with trauma and life-long disabilities, according to the UN children`s agency, UNICEF.
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