The casket — covered in flowers and featuring a huge portrait of the 27-year-old striker — was accompanied by Benitez's wife, Liseth Chala, and other relatives.
Officials from Benitez's Qatari club El Jaish and several players also came to the airport to say their final goodbyes.
"We would like to convey our greatest condolences to the family of the bereaved, and also to El Jaish club and also to all Ecuadorean fans," Qatari league deputy CEO Hani Ballan said. "Benitez was one of the well-known players and really one of the top players."
Benitez joined El Jaish in July. The club said he died Monday of heart failure, a day after playing his first match for the club. Ecuador officials said Benitez was taken to the hospital with sharp stomach pains, developed peritonitis and died of cardiorespiratory arrest.
El Jaish said Thursday that Benitez had complained of stomach pains but described him as strong and healthy. The club said Benitez passed a medical on July 4 and didn't complain of any health problems during Sunday's match, when he came on as a second-half substitute.
"I don't think it was anything else, apart from heart attack, and a heart attack could happen any time, to a healthy or unhealthy person, and we know that he was a very healthy person, he is a strong player, and this is just a heart attack," El Jaish vice chairman Nasser Mohamad al-Ali said.
Hours after the flight left, El Jaish took the pitch against Al Shahaniya in the first match since his death in a pre-season tournament known as the Sheik Jassim Cup. There was a minute's silence for Benitez. The players wore black arm bands in memory of him and the team held a huge sign before the match with the striker's portrait and the words "Christian Benitez We Will Miss You."
The match ended in a 4-4 draw.
The plane carrying Benitez's body is expected to arrive in Ecuador around midnight local time after stopping in Portugal. A funeral is scheduled for Friday in Quito, along with separate tributes to the former America and Birmingham player.
Benitez scored 24 goals in 58 appearances for Ecuador and was in its 2006 World Cup squad. He also scored against Chile in the 2007 Copa America and scored four goals during qualifying for the 2014 World Cup.