The weekly newspaper said running the advert was "meant as a purely humanitarian gesture".
When it launched the appeal, the DEC said the latest conflict had made half a million people in Gaza homeless and warned of a "humanitarian emergency".
There is currently a five-day ceasefire between Israel and the Palestinians.
The Israelis launched a military operation on 8 July to stop militant attacks from Gaza.
After a DEC advert featured in this week's Jewish Chronicle (JC), a Facebook page was set up calling on readers to boycott the title until it issued a "full apology".
A message posted on the paper's own Facebook page pointed out that the advert was "not an expression of the JC's view".
It added: "We have received complaints from readers angry at the decision. We apologise for the upset caused."
It said it would give space in the next issue to readers wanting to object to the advert.
Writing on the JC website, editor Stephen Pollard said: "It is a critical part of our editorial independence that we do not allow advertisers to have any influence at all on the paper."
About 2,000 people have died since the fighting began last month.
Those killed include more than 1,900 Palestinians, mostly civilians, according to the United Nations. Sixty-four Israeli soldiers have been killed in the violence and three civilians in Israel have also died.
The DEC, an umbrella organisation which brings together 13 UK aid charities to deal with international crises, launched its campaign on 7 August. It said one and a half million people had "no or very limited" water or sanitation, with many in "urgent need of medical care".
The BBC and other public service broadcasters agreed to air a DEC Gaza appeal.
In 2009, the BBC and Sky chose not to broadcast a previous Gaza appeal, with the BBC's decision prompting angry protests and 40,000 complaints.
In a statement on the DEC's website on Thursday, addressing the "tone of the debate over Gaza", chief executive Saleh Saeed said: "The DEC's launch of a public appeal in response to the humanitarian crisis in Gaza has been wrongly interpreted in some quarters as a political statement.
"It is nothing of the sort. Giving aid is not taking sides."