Palestinian officials blamed an Israeli air strike for the fireball that engulfed the Al-Ahli al-Arabi hospital on Tuesday evening, which they said had killed 471 people.
Israel said the blast was caused by a failed rocket launch by the Palestinian Islamic Jihad militant group, which denied blame.
Arab leaders responded to the loss of life, which they blamed on Israel, by cancelling a summit with Biden in Jordan.
This had been intended as the second half of his carefully choreographed itinerary for emergency meetings with allies to avert a wider war in the region.
Speaking alongside Israeli Prime Minister Benjamin Netanyahu, Biden said: "I was deeply saddened and outraged by the explosion of the hospital in Gaza yesterday, and based on what I've seen, it appears as though it was done by the other team, not you."
"But there's a lot of people out there not sure, so we've got a lot, we've got to overcome a lot of things," Biden added.
Biden later said his comment was based on information he had been shown by the US Department of Defense, without elaborating further.
Biden's trip to the Middle East was designed to calm the region, even as he demonstrated US support for its ally Israel, which has vowed to annihilate the Hamas movement whose fighters killed 1400 in Israel in a rampage on October 7.
But after the hospital blast, Jordan cancelled the planned Amman summit where Biden had been due to meet the leaders of Jordan, Egypt and the Palestinian Authority.
Instead, he was expected to speak to the Jordanian and Egyptian leaders by phone from Air Force One on the way home.
Netanyahu thanked Biden for his "unequivocal support".
After his talks with Netanyahu's war cabinet, Biden held an emotional meeting with Israeli survivors of the October 7 rampage.
He hugged retired grandmother Rachel Edri, who was held hostage at gunpoint in her home for 20 hours by Hamas and used food and conversation to stall them until their capture.
"Please keep supporting us in eliminating Hamas once and for all," a soldier told Biden.
The accounts of destruction at the hospital were horrific even by the standards of the past 12 days, which have confronted the world with relentless images, first of Israelis killed in their homes and then of Palestinian families buried under rubble from Israel's retaliatory strikes.
Rescue workers scoured blood-stained debris for survivors.
A Gaza civil defence chief gave a death toll of 300 while the health ministry put it at 471, although Israel disputed those figures.
Palestinian ministry representative Ashraf Al-Qudra said rescuers were still recovering bodies.
Israel later released drone footage of the scene of the explosion, which it said showed it was not responsible because there was no impact crater from any missile or bomb and no structural damage to surrounding buildings.
The Israeli military published what it said was an audio recording of "communication between terrorists talking about rockets misfiring".
Palestinians were convinced the explosion was an Israeli attack, with no warning for civilians to leave a hospital being used as a shelter by Gazans already made homeless by bombing.
A doctor, Ghassan Abusittah, said the hospital had shaken all day because of bombing.
He heard the sound of a missile just before a huge explosion and then the operating room ceiling collapsed.
In the courtyard he said he could see bodies and limbs everywhere.
Abusittah said he then treated a man whose legs were blown off.
A Gaza civil defence chief said 300 people were killed in a hospital explosion.
World leaders from United Nations Secretary General Antonio Guterres to Russian President Vladimir Putin denounced the blast in statements that nonetheless avoided addressing who was to blame.
As Biden wrapped up his visit, Netanyahu's office put out a statement saying Israel would let food, water and medicines reach southern Gaza via Egypt.
It reiterated that it would not let aid in from Israel until Hamas released its hostages.
