The demonstration was the third show of solidarity organised by residents of Doha in just one week, where solidarity processions have been held across the capital.
"We stand here today to tell them, the blessed Al Aqsa mosque is a red line, remove your filthy hands from Jerusalem, the Al Aqsa Mosque and our people in Sheikh Jarrah," Haniyeh told the demonstrators.
"Netanyahu, do not play with fire," he warned.
Several cities across the world witnessed similar action on Saturday to denounce the worst Israeli violence since the 2014 war in Gaza.
In London, several thousand protesters carrying placards reading "Stop Bombing Gaza" and chanting "Free Palestine" converged on Marble Arch, near the British capital's Hyde Park, to march towards the Israeli embassy.
In Madrid, some 2,500 people, many of them young people wrapped in Palestinian flags, marched to the Puerta del Sol plaza in the city centre.
"This is not a war, it's genocide," They chanted.
"They are massacring us," said Amira Sheikh-Ali, a 37-year-old of Palestinian origin.
"We're in a situation when the Nakba is continuing in the middle of the 21st century," she said, referring to the "catastrophe" word used by Palestinians to describe the ethnic cleansing campaign carried out during Israel's creation in 1948, when hundreds of thousands fled or were driven out.
"We want to ask Spain and the European authorities not to collaborate with Israel, because with their silence, they are collaborating," said Ikhlass Abousousiane, a 25-year-old nurse of Moroccan origin.
Israeli air and artillery strikes on Gaza since Monday have killed 139 people including 39 children, and wounded 1,000 more, health officials in the coastal enclave say.
On Saturday, Israeli airstrikes on Gaza destroyed a 13-storey building housing the Qatar-based Al Jazeera broadcaster as well as US news agency The Associated Press.
''It is clear that those who are waging this war do not only want to spread destruction and death in Gaza, but also to silence media that are witnessing, documenting and reporting the truth of what is happening in Gaza,'' said Walid al-Omari, Al Jazeera's Jerusalem bureau chief.
''But this is impossible,'' he said on air shortly after the 13-storey Jala Tower in Gaza was obliterated.
''This is a crime among a series of crimes perpetrated by the Israeli army in the Gaza Strip.''
President and CEO Gary Pruitt said the AP was "shocked and horrified" by the strike.
"They have long known the location of our bureau and knew journalists were there. We received a warning that the building would be hit," Pruitt said in a statement.
"This is an incredibly disturbing development. We narrowly avoided a terrible loss of life. A dozen AP journalists and freelancers were inside the building and thankfully we were able to evacuate them in time," he added.
Footage showing the building collapsing to the ground after the Israeli air strike, sending up a huge mushroom cloud of dust and debris, was broadcast live on Al Jazeera.
Jawad Mehdi, the owner of the Jala Tower, said an Israeli intelligence officer warned him he had just one hour to ensure the evacuation of the building.
Al Jazeera's correspondent in Gaza, Safwat al-Kahlout, tweeted his despair over the destruction.
''I have been working here for 11 years. I have covered many events from this building... now everything, in two seconds, just vanished,'' he said.
Israel alleged its "fighter jets attacked a high-rise building which hosted military assets belonging to the military intelligence of the Hamas terror organisation".
"The building also hosted offices of civilian media outlets, which the Hamas terror group hides behind and uses as human shields," it said.
Al Jazeera has said it will take legal action against the Israeli military over the strike.