The Spanish champions have agreed to pay the South Korean promoters of the first game 200,000 euros in compensation after Messi played just 17 minutes against a K-League select XI on Wednesday.
The World Player of the Year played all 46 minutes of the first half on Sunday and Barcelona coach Pep Guardiola denied he had been pressured into keeping the Argentine forward on the pitch.
"If there had been pressure I would have let him play 45 minutes in Korea," he told reporters. "The arrangements are made according to tactical requirements. Seeing him in training, he was fit enough to play the entire half."
Messi's presence was all the more important after Barcelona travelled to Asia without any of their eight Spanish World Cup winners - the absence of Xavi in Seoul costing them another 100,000 euros in compensation.
Returning to the stadium where he won Olympic gold with Argentina in 2008 and cheered at every touch, Messi made every effort to provide the crowd with the goal they wanted but was twice denied by China goalkeeper Yang Zhi and once by the post.
"He needs time to recover from the World Cup, he's only had four or five days intensive training," Guardiola added.
Messi's less well known team mates provided the first half scoring, with Sergi Roberto finding the net after 10 minutes and Nolito doubling the advantage three minutes later by volleying home from an angle.
Beijing had their chances too and Australian brothers Joel and Ryan Griffiths were both robbed of opportunities by bobbles on a pitch which was a disgrace to the splendour of the stadium.
"I hope on our next visit, this world class stadium has a better pitch," said Guardiola. "World class performances need world class pitches."
Messi departed to be replaced by Ibrahimovic at half-time and, with the high humidity unrelenting, Beijing looked the livelier of the two teams without being able to exploit their chances.
Swedish striker Ibrahimovic, the only other name in the Barcelona team sheet familiar to most of the crowd, slotted home the final goal of the night from just outside the area a minute from the end.
"Ibrahimovic has only got half a game in him at the moment," explained Guardiola. "I needed to balance the first and second half so I had Messi start and Ibrahimovic as the substitute."
The match, played out in front of a half-full stadium, was the highlight of China's second National Fitness Day, which marks the anniversary of the opening of the 2008 Beijing Olympics.
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