"Waqar Younis has resigned as Pakistan's head cricket coach," Pakistani media agencies were quoted as saying.
Pakistan failed to qualify for the semi-finals of the marquee tournament, losing three successive group phase matches.
Earlier last week, Younis begged forgiveness and offered to resign from the post.
The former-Pakistan captain's resignation comes a day after Team's skipper Shahid Afridi announced he is stepping down as the captain of the Pakistan T20 cricket team on his own will but intends to continue playing for the country.
Waqar, had earlier said, the team will not improve unless the whole system is changed and made transparent.
At a press conference outside the Pakistan Cricket Board (PCB) office in Lahore, Waqar said that "apparent makeup surgery will not work".
"I apologise for the team's performance in the T20 World Cup," he was quoted as saying by nation.com.pk, but warned against any knee-jerk reaction.
"The matter will not be solved, if we blame single individuals, whether it's me, (Shahid) Afridi or the PCB chairman. We have to find the real inner problems."
He said there is a need to sit down and talk to find long-term solutions, but added that he's willing to resign if that is believed to be the solution.
"If things will improve if I leave, then I am ready to go home," he said.