MORE: Masterful Younis frustrates Australia
Pakistan reached 219-4 at stumps after the first day's play in Dubai on Wednesday, recovering well after falling to 7-2 early on.
A century from Younis Khan led the Pakistan revival, with Johnson's 3-22 from 20 overs comfortably the best bowling figures in the Australia attack.
Johnson struck in the very first over, removing Mohammad Hafeez lbw, before having Azhar Ali caught at cover midway through the day.
After Australia had taken the second new ball at the first available opportunity, Johnson dismissed Younis with his second delivery, and the left-armer knows he and his team-mates must begin strongly on Thursday.
"We have to turn up and start pretty well," he said looking ahead to Thursday's play. "The ball is still pretty new and in good condition as well, so the first couple of overs are going to be important for us in the morning.
"You have really got to use that new ball and make them play early on.
"We knew we had to focus on getting the ball up there, hit guys on the pads or get nicks early on.
"I think we stuck to our plan and didn't go away from it, I'm really happy with how we went about it today.
"Guys just have to be patient and that's what we did today, we worked as a bowling unit, we were patient and didn't let them get away.
"We are happy to be in this position and we just need to get ourselves right and turn up in the morning."