Sydney FC meanwhile claimed a 1-1 draw with Yokohama F. Marinos by holding the group toppers from Japan despite finishing bottom with five points from six matches, which included just one win.
With Shanghai SIPG and Yokohama F. Marinos already in the last 16, Friday's matches were only meant to complete the formalities.
At the Khalifa International Stadium, Jeonbuk were served well by Cho Gue-sung whose first-half double helped the South Koreans establish an early foothold on the match against the Chinese giants who fielded several untested players.
Cho put Jeonbuk ahead in the 16th minute with a header from the centre of the box from a measured cross from Lee Sung-hoon, catching the Shanghai SIPG defence with surprise.
As Shanghai SIPG struggled to gain control, Jeonbuk consolidated their advantage, scoring from a penalty in the 32nd after another Lee pass found Cho, but his shirt was pulled preventing him from taking a shot.
Cho fired home with a confident shot from the spot to give the Koreans a comfortable cushion, which they maintained until the end.
Jeonbuk's Portuguese coach Jose Morias was in a positive mood after the three points despite coming to the end of his contract with the side, having already announced his intention to move back to Europe after leading them to the K League title last month.
"Today I am smiling for the effort of the players and because it was our last game together. It's good to end things with a positive memory," said Morais who has worked as Jose Mourinho's assistant at Inter Milan, Real Madrid and Chelsea.
"I believe in the future of the club. Some of the young players in the team have a lot of quality and I know the club has the right set-up to enable them to be successful."
Shanghai SIPG coach Vitor Pereira said he was forced to give inexperienced squad members game time because of the tight schedule of the competition.
"We lost today but we played six young players, a lot of them without even one minute in the competition or in the Chinese League," said Pereira.
"It means it was their first game of the season. I think they did well. We know it's impossible to play six games in 15 days," the Portuguese boss added.
Sydney FC coach Steve Corica was also looking at the positives.
"I am very pleased with the performance and I thought we were a little unlucky not to get the win in the end," said Corica.
"I think Yokohama will go a long way in this tournament, so I wish them all the best."