The ministry said damage to the Aramco Tower was limited and there were no injuries or fatalities, without assigning responsibility for the attack.
The Saudi-led coalition fighting Iran-aligned Houthis in Yemen said Saudi air defences had intercepted Houthi missiles over the city in the early hours.
The Houthis, who later claimed responsibility for the attack, have escalated their fighting with the kingdom in what has become another front in the wider US-Israeli war with Iran.
Many schools in the kingdom resumed in-person classes on Sunday after weeks of home learning and several Saudi government agencies returned to in-office work suspended after earlier Houthi attacks.
The Houthis have ramped up strikes on Aramco facilities in recent weeks, including the oil giant's headquarters in Dhahran in the Eastern Province of Saudi Arabia.
The Saudi-led coalition said air defences also intercepted a Houthi missile on Sunday in the province, where most of the oil and gas reserves of the world's largest crude exporter lie.
It said in two separate statements that it had also destroyed ballistic missile launchers in Saada and Sanaa used by the Houthis in Sunday's attacks on Riyadh and the Eastern Province.
The renewed fighting between the Houthis and the coalition backing Yemen's internationally recognised government intensified after the Houthis advanced in September toward the Bab el-Mandeb Strait, a strategic shipping chokepoint on the other side of the Arabian Peninsula from the Strait of Hormuz.
The Houthis have since stepped up missile and drone attacks on Saudi ports and airports, including Riyadh's international airport.
The latest escalation comes a day after Yemen's Houthi-run health ministry reported Saudi air strikes near Sanaa, where at least 40 people were killed in the attacks. Saudi authorities said they were investigating.
Houthi military spokesperson, Yahya Saree, said the airport was targeted in Sunday's attacks, but there was no confirmation from Saudi authorities.
In response to the attacks, Saudi Arabia has been carrying out air strikes against Houthi targets in Yemen.
The kingdom, a key American ally, has also been requesting assistance from the US and a number of countries in Europe and the Middle East, seeking both defensive and offensive support against the Yemeni group.