One newspaper captioned the picture "the height of humiliation" [Image: Lior Mizrahi/Israel Hayom]
Israel has apologised to Turkey in an effort to defuse a row over the treatment of its envoy in Tel Aviv.
Israel's prime minister said he hoped this "would end the affair".
Ankara had threatened to withdraw the ambassador unless it received a formal apology from Israel by Wednesday evening.
The row began when the envoy was summoned to Israel's foreign ministry over a Turkish TV series portraying Israeli agents kidnapping babies.
Deputy Foreign Minister Danny Ayalon summoned Ambassador Oguz Celikkol to rebuke him over the fictional television series Valley of the Wolves, popular in Turkey.
Mr Ayalon ensured the ambassador was seated on a lower chair and removed the Turkish flag from the table.
Turkish President Abdullah Gul said the ambassador would "return on the first plane" on Thursday unless Israel issued a public apology.
In the letter of apology, Israel's Prime Minister Benjamin Netanyahu "again expressed his concern over the cooling of the ties between Israel and Turkey" and instructed officials "to find ways to prevent this trend", according to a statement from his office.
The Turkish Prime Minister Recep Tayyip Erdogan said Turkey had received the apology it "wanted and expected in diplomatic terms."
But at a news conference he added that "Israel must put itself in order and must be more just and more on the side of peace in the region."
Footage of Mr Ayalon urging journalists to make clear the ambassador was seated on a low sofa, while the Israeli officials were in much higher chairs, has been widely broadcast by the Israeli media.
He is also heard pointing out in Hebrew that "there is only one flag" and "we are not smiling".
Jonathan Head, BBC News, Istanbul
The diplomatic stunt had the potential to escalate into a serious breach between Israel and Turkey.
Clear splits have emerged within Israel's coalition government over how to handle the Turkish government, which has become an increasingly strident critic of Israel at the same time as it has moved closer to Iran and Syria.
It is less clear what Turkey's long-term aims are with Israel, for decades a close military and trading partner, but the governing party has said it no longer sees its relationship with Israel as a priority.
"In terms of the diplomatic tactics available, this was the minimum that was warranted given the repeated provocation by political and other players in Turkey," he said, according to Reuters.
One Israeli newspaper marked the height difference in a photo, and captioned it "the height of humiliation".
Last October Israel complained over another Turkish series, which depicted Israeli soldiers killing Palestinians. In one clip, an Israeli soldier shoots dead a smiling young girl at close range.
The row comes ahead of a planned visit by Israeli Defence Minister Ehud Barak to Turkey on Sunday.
Turkey has long been an ally of Israel, but relations have deteriorated as Ankara has repeatedly criticised Israel for its offensive in Gaza a year ago.
Rights groups say about 1,400 Palestinians died during the operation, which Israel said had been aimed at ending rocket fire by Hamas.
Thirteen Israelis died during the violence.