He took three wickets in the Edgbaston Test which Australia won by 251 runs to take a 1-0 lead in the five-match series.
"I think what we've done in the past with James is got him back, we know how good he is so we keep using him and keep bowling him and eventually he's broken again," cricket.com.au quoted Paine as saying ahead of the Lord's Test.
Pattinson will be replaced by either Josh Hazlewood, who has also returned from a serious back injury, or Mitchell Starc.
"We're really lucky in the fact we've got two bowlers (Starc and Hazlewood) in particular on the sidelines that are world class and we want to make sure James is absolutely cherry ripe every time he plays.
"He's available for selection but we've decided to rest him for this game and make sure that his long-term future is in really good shape," he added.
The Australia skipper further indicated that Pattinson would be playing in the third Test beginning August 22.
"It was always going to be one way or the other - (Pattinson) would miss this Test and be fresher for the third Test or he has this one after the long break and doesn't play in the third," Paine explained.
"If you look at Mitchell Starc and Josh Hazlewood's records at Lord's, it's a good venue for one of those to play and be confident in the fact they can bowl really well here," he added.
Australia's 12-man squad for the Lord's Test David Warner, Cameron Bancroft, Usman Khawaja, Steve Smith, Travis Head, Matthew Wade, Tim Paine (c, wk), Pat Cummins, Mitch Starc, Peter Siddle, Nathan Lyon, Josh Hazlewood