Prince Charles shook hands with Zimbabwean President Robert Mugabe. Charles, seated one place away from the president, was "caught by surprise" when Mugabe leaned over to greet him, Clarence House said.
President Mugabe side-stepped a European Union travel ban to attend the service in Rome.
President George Bush and French President Jacques Chirac divided over the US-led war in Iraq were separated only by their wives as they sat in the second row to the right of the altar in front of St Peter's Basilica.
Farther down the same row was Iranian President Mohammad Khatami, who greeted Syrian President Bashar Assad before taking his seat. Washington has tense relations with Syria and none with Iran.
More than 100 official delegations attended the funeral, one of the largest religious gatherings of modern times. The seating plan was drawn up using French, the traditional language of diplomacy.
Just making it onto the front row was King Juan Carlos of Spain Espagne ahead of the president of the United States Etas-Unis in the second.
The gathering made for a rare display of religious plurality: scarlet-robed Catholic cardinals, black-clad Orthodox clerics, Arab head scarves, Jewish skull caps, Central Asian lambskin hats, and black veils worn by some women.
However, the funeral also sparked diplomatic tensions.
China refused to send a delegation to the funeral because of the Vatican's diplomatic relations with rival Taiwan, whose president, Chen Shui-bian, took advantage of a rare chance to meet other leaders at an international event.
When Bush's face appeared on giant screens showing the ceremony, many in the crowds outside St Peter's Square booed and whistled.
In one of the remarkable expressions of temporary accord, Israeli President Moshe Katsav met the leaders of arch-enemies Syria and Iran at the funeral.
Katsav twice shook hands with Syrian President Bashar Assad, Israeli media reported, the second time initiated by Assad.
Also, the Iranian-born Israeli president briefly spoke with Iranian President Mohammed Khatami in Farsi. According to Israel Radio, the two talked about the town where both men were born.
Israel accuses Syria and Iran of backing Palestinian militants in the West Bank and Gaza Strip. Israel has also been a leading critic of Iran's nuclear programme.