According to the Egyptian presidency, El-Sisi praised Qatar’s crisis handling and commended its air defence systems' capabilities for intercepting Iranian missiles.
He also lauded the Qatari leadership’s “prudence and wisdom” in responding to the attack.
The two leaders discussed regional developments, including efforts to reduce tensions between Iran and Israel.
They also discussed ongoing coordination between Cairo and Doha to secure a ceasefire in the Gaza war.
The Iranian strike on Al-Udeid — the largest US military base in the Middle East — took place on Monday, in what Tehran described as retaliation for American airstrikes on nuclear sites in Iran.
The US base had been evacuated as a precaution ahead of the attack.
The Iranian attack on Al-Ubeid triggered temporary airspace closures in Qatar and Arab Gulf states, but flights were resumed shortly after.
Qatar and the Gulf Cooperation Council condemned the Iranian attack on Al-Ubeid as a flagrant breach of its sovereignty.
"We affirm that the State of Qatar reserves the right to respond directly in a manner proportional to the nature and scale of this blatant aggression," foreign ministry spokesman Majed Al-Ansari stated.
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