An Arab diplomatic source had earlier told AFP on condition of anonymity that the Iraqi government had invited Sharaa for the meeting planned for Saturday but that he would not attend.
The Syrian presidency statement said that Sharaa "will not participate" in the summit, adding that the Syrian delegation would be headed by Shaibani, who "will represent Syria in the discussions and talks that will take place during the meeting".
Sharaa, whose Islamist group spearheaded the offensive that toppled Syria's longtime ruler Bashar al-Assad in December, was imprisoned for years in Iraq on charges of belonging to Al-Qaeda following the 2003 US-led invasion.
Several powerful Iraqi politicians had voiced opposition to Sharaa's planned visit to Iraq.
They include former prime minister Nuri al-Maliki, a leading member of Iraq's main pro-Iran coalition that holds a parliamentary majority.
Armed groups aligned with Tehran had also joined the call against Sharaa, including the powerful faction Kataeb Hezbollah which previously fought in Syria alongside Assad's forces.
Several Iraqi security sources told AFP that an old arrest warrant for Sharaa from his time as a member of Al-Qaeda remains in place.
However, authorities seek good relations with Syria's new leadership to help maintain regional stability, the sources said.
The fall of Assad, who was a close ally of the government in Baghdad, has complicated relations between the neighbouring countries.
Iraq, where the majority are Shiite Muslims, remains deeply scarred by decades of conflict following the US-led invasion, which triggered sectarian violence and the rise of Sunni jihadist groups including Al-Qaeda and the Islamic State.
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