The admission is contained in the Israeli response to the Goldstone report, which concluded both Israel and Hamas had committed war crimes.
Both officers have retained their ranks according to reports.
Until now the Israeli army has denied breaking the rules of engagement over the use of white phosphorus.
During the 22-day conflict last year media pictures showed incendiary shells raining down on a UN compound.
Several artillery shells were fired in violation of the rules of engagement prohibiting use of such artillery near populated areas
Israeli response to the UN Goldstone report
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The officers were named in Israeli media reports as Gaza Division Commander Brig Gen Eyal Eisenberg and Givati Brigade Commander Col Ilan Malka.
"Several artillery shells were fired in violation of the rules of engagement prohibiting use of such artillery near populated areas," the report says.
The officers were charged with "exceeding their authority" in ordering the use of the weapons in an attack on 15 January 2009.
An Israeli Defence Force spokesman said that the reprimand would be noted on their records and would be considered if they apply for promotion in future.
Brig Gen Eisenberg is still in command of Israel's Gaza division, and Col Malka has been moved to the West Bank under the same rank, according to the Reuters News Agency.
'Hush money'
A Hamas spokesman said the disciplinary action was "further admission of Israel's guilt" over alleged war crimes.
But he said he did not expect any further action to be taken against military officers.
He said Israel had paid the UN $10.5 million (£6.6 million) in damages to repair their compounds, which he called "hush money".
A UN representative who was in the compound in Gaza city during the attack told the BBC he "expected full accountability from the Israelis".
Two UN staff and two Palestinians sheltering in the compound were seriously injured he said.
A doctor at Gaza city's main hospital told the BBC he treated hundreds of Palestinians for phosphorus burns during the offensive.
'Buried'
The BBC's Paul Wood in Jerusalem says it is the first time Israel has revealed it reprimanded any officer for their actions during the offensive, named by the Israeli military as Operation Cast Lead.
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This is the first time that Israel has acknowledged allegations by the UN and other international organisations that white phosphorus was used in such a way as to endanger civilians during the Gaza war.
Our correspondent says the admission was buried in the document handed to the United Nations on Friday.
The UN General Assembly has demanded that both Israel and Hamas launch independent investigations into their conduct during the Israeli operation which began in December 2008.
An Israeli official said the submission to the UN was not intended to respond in detail to the allegations and incidents outlined in the Goldstone report, but to explain why the Israeli justice system was "reliable" and "independent".
The Islamist movement Hamas has denied that its forces deliberately targeted civilians with rockets.
Both sides have until 5 February to respond in detail to the UN General Assembly's request for independent investigations to be launched.
White phosphorus, which is used to lay smokescreens, is legal for use on open ground but its use in built-up areas where civilians are found is banned under international conventions.
'Repeated use'
Pictures showed chunks of brightly burning phosphorus, streaming white smoke, landing on the UN compound.
The UN compound was severely damaged and people sheltering there were injured.
Human Rights Watch, the New York based rights group, said Israel's use of phosphorus weapons was more widespread and many people had died as a result of burn injuries.
Its report concluded that the Israeli military "repeatedly exploded white phosphorus munitions in the air over populated areas, killing and injuring civilians and damaging civilian structures, including a school, a market, a humanitarian aid warehouse and a hospital".
In March the Israeli Defence Force issued a written statement in response to these allegations.
"Based on the findings at this stage, it is already possible to conclude that the IDF's use of smoke shells was in accordance with international law. The claim that smoke shells were used indiscriminately, or to threaten the civilian population, is baseless," it said.
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