Forward Juan Belencoso, who recently signed a two-season extension with the club, scored Kitchee's first goal in the 32nd minute with a powerful header.
Midfielder Lam Ka-wai doubled Kitchee's lead in the 44th minute when his shot from 20 yards could not be stopped by Persib goalkeeper I Made Wirawan.
"I feel sorry to leave such a good team," Molina told the South China Morning Post. "We pressed hard in the first half and our effort paid off.
"We held back a bit after the break as we were two goals up and the intimidating atmosphere also made our life very difficult.
"I am very happy to walk away with such an important win in my last match with Kitchee."
Meanwhile, Kitchee captain Lo Kwan-yee believes that his side outplayed Persib and added that he was glad to have a 2-0 lead at half-time.
"The temperature was not too hot and humid and we were not disadvantaged," he said. "We were able to use the ball well and took the opportunities to lead by two goals. They tried to come back in the second half and put us under a lot of pressure, but we were well prepared and hung in there till the end."
With Kitchee having reached the last eight, Lo already has his eyes set on the final after his side were beaten 3-2 on aggregate by Erbil in the semi-final last year.
"The result gives us a lot of confidence to go one better than last year and reach the final," he said.