Global, who were beaten by Yadanarbon 2-0 when both sides met on March 18, found themselves 1-0 up in the 16th minute after Mark Hartmann scored from the penalty spot.
However, Yadanarbon only had to wait for three minutes before the scores were level once again thanks to Yan Paing's goal.
But, Hartmann put the Filipino champions in front for the second time in the match when he slotted the ball into the bottom corner in the 40th minute.
Following the break, Global came out all guns blazing and continued to look extremely threatening.
They were rewarded for their aggressive approach and mindset in the 60th minute when Misagh Bahadoran went on a weaving run before going on to beat goalkeeper Thiha Sithu to make it 3-1.
To make matters worse for Yadanarbon, Zaw Lin Tun and Tin Win Aung were both shown red cards just minutes apart.
With only nine men left standing, Yadanarbon tried to contain Global and stop them from scoring again.
However, their plan collapsed when Global broke through and Renato Gonzalez scored to make it 4-1 in the 83rd minute.
As a result of the win, Global are now level with Pahang, who were beaten 3-1 by South China, on the Group G standings with four points.
"It feels good to win and make history," Padernal told the official AFC website. "We were able to prove that we can play at this level. The training and preparation showed in the game. The players showed a lot of heart.
"The group is now wide open with South China winning. We know that we have a good chance of making the knockout stage."
Meanwhile, Yadanarbon coach Kyi Naing attributed his side's loss to the fact that they didn't have a full-strength squad.
"I cannot fault the team with their performance because they played hard," he said. "Our best defender Happiness (Okpechi) did not play and it made it difficult for us.
"The current situation is very difficult with so many players injured and with suspensions. We will just do the best that we can to finish the group stage."