In a video message Zelensky said he had "decided to replace the commander of the air force" to strengthen Ukraine's military leadership.
His office earlier published a presidential decree to officially remove Mykola Oleshchuk from the post.
The crash of the F-16 was a high-profile setback for Kyiv, which had lobbied the West to send the advanced fighter jet for months.
It was the first reported loss, just weeks after Ukraine first started taking delivery of the supersonic aircraft.
The military had said the plane and pilot crashed during a combat mission earlier this week after having shot down incoming Russian missiles.
Lawmaker Mariana Bezugla, who sits on a parliamentary defence, security and intelligence committee, claimed the F-16 was shot down by Ukraine's own air defence systems in a case of friendly fire.
In response to those allegations Oleshchuk earlier on Friday accused her of trying to discredit Ukraine's military leaders, and said a full investigation into the incident was underway.
Zelensky did not provide further details on why he had decided to replace his air force commander, saying only that his command team "needed to get stronger".
Lieutenant General Anatolii Kryvonozhko, who leads the air force's operations in the central part of Ukraine, would temporarily assume the role of overall commander, the air force said.
It is not the first time Zelensky has removed a senior military leader.
Earlier this year he removed popular commander-in-chief Valery Zaluzhny.
He was replaced with Oleksandr Syrsky, who masterminded leading Ukraine's shock counter-attack into Russia's western Kursk region.
Top Ukrainian military pilot dies after F-16 fighter jet crashes
Washington DC (UPI) Aug 29, 2024 -A top Ukrainian fighter pilot has died following the crash of a U.S.-made F-16 fighter jet Monday, authorities announced.
Pilot Oleksiy Mes, known by his piloting call sign "Moonfish," was killed in the crash while "repelling the biggest ever aerial attack" by Russia against Ukraine, said a Ukrainian military source, who added that Mes was buried on Thursday, CNN reported.
Ukrainian officials have said they do not believe pilot error was behind the accident. The cause of the crash is being investigated.
"During the approach to the next target, communication with one of the aircraft was lost. As it turned out later, the plane crashed, the pilot died," the Ukrainian General Staff said in an update Thursday.
The arrival of the U.S. made F-16s had been highly anticipated in Ukraine as the country continues to seek military resources from its allies in its war against Russia's invasion, which has dragged on for more than 2.5 years. The planes arrived in Ukraine earlier this month and the pilot who died was among the only Ukrainian aviators trained to fly the F-16.
President Volodymyr Zelensky has said the Ukrainian Air Force used the F-16 to destroy missiles and drones launched by Russia earlier in the week, the first time an official confirmed the F-16s were being used in combat.
Reports indicate the plane piloted by Mes went down amid a barrage of Russian missiles, but that the Ukrainian F-16 destroyed three cruise missiles and a Russian drone in the largest attack on Ukraine yet, a statement said.
"Oleksiy saved Ukrainians from deadly Russian missiles," the Ukrainian Air Force wrote in a statement on social media. "Unfortunately, at the cost of his own life."
Mes and a fellow Ukrainian F-16 pilot, Andrii (Juice) Pilshchykov, appeared before Congress in June 2022 to push for the planes to be sent to Ukraine.
"When I met with Ukraine pilots Juice and Moonfish I had a sick feeling they wouldn't make it through the war," former U.S. congressman Adam Kinzinger posted on X. "They fought like hell for Ukraine, and the F16."
Pilshchykov, aka Juice, died on a mission last August.
The United States and NATO allies have pledged about 65 F-16s to Ukraine, which has now also asked allies for the approval to use long range missiles, too.
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