Kitchee took the lead in the 27th minute through Juan Belencoso's magnificent header and doubled it just eight minutes later when Jordi Tarres scored.
The 2-0 victory keeps Kitchee atop the Group F standings with seven points from three matches.
However, Molina acknowledged the fact that the Hong Kong-based club will be in for a much tougher challenge in the second leg, which will be held in Malaysia.
"It was a really good match. In the second half they pressed us a little bit more, but I think it was a good half too and the players did very well," Molina told the official AFC website. "We know it will be different away from home but we will try to do the same, play good football and, of course, always try to win. The first aim is to qualify but we would like to qualify first and we are in that position now.
"We will have a tough match in Malaysia but I have confidence in my players and my team."
While Johor coach Bojan Hodak was pleased with his side's performance, he did point out that they need to improve on their finishing.
"It was a good game, I think the fans enjoyed it because of the way we both play football," he said. "I think we both created chances only they scored theirs.
"Overall, I’m happy with the way my team played, but we need to improve our finishing. Everything is still open in the competition."