The Wembley Stadium arch will not be lit in the blue and white of the Israeli flag.
The Football Association says that instead England and Australia players will wear black armbands during their friendly at Wembley on Friday night.
A period of silence will also be held before kick-off.
In a statement, the FA said it will “remember the innocent victims of the devastating events in Israel and Palestine”.
“Our thoughts are with them, and their families and friends in England and Australia and with all the communities who are affected by this ongoing conflict. We stand for humanity and an end to the death, violence, fear and suffering.”
Israel prepares for ground invasion – follow live conflict updates
It added that it will only allow flags and kits of competing nations inside Wembley during England’s game against Australia on Friday, and the Three Lions’ clash against Italy on 17 October.
Over the years, the Wembley arch has been illuminated in the colours of the flags of countries, including France, Turkey and Ukraine, within days of attacks.
There are clear sensitivities – with some wanting Palestinian deaths acknowledged.
The president of the FA – Prince William – has commented on the situation in a joint statement with his wife through a Kensington Palace spokesperson.
In part it read: “As Israel exercises its right to self-defence, all Israelis and Palestinians will be continued to be stalked by grief, fear and anger in the time to come.”
Health Secretary Steve Barclay had earlier joined calls for the Wembley arch to be lit up in blue and white on Friday, telling Sky News “we should make clear our strong support for Israel”.
“We stand with Israel, and I think we’ve seen that with Parliament, we’ve seen it with Number 10,” he said. “I think it would be fitting to show that with Wembley as well.”
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Barclay: ‘Hamas are responsible’
Asked what sympathy he has with the people of Gaza, he said the UK “does have sympathy” and contributes “about 10%” of the aid distributed in the region through the United Nations.
“It’s why the foreign secretary was in Israel yesterday talking to counterparts about the importance of minimising civilian casualties,” he added.
Latest figures from the Israeli Defence Forces (IDF) show at least 1,300 Israelis have died and more than 2,700 injured since Hamas’s surprise attack on Saturday.
The Gaza Health Ministry, meanwhile, reports at least 1,354 Palestinians have died and 6,049 injured in Israeli strikes.
