The in-form Leon Bailey went close to a stunning equaliser when he struck the crossbar nine minutes after the break and Bayern soon made the most of that, as Ribery rounded off a swift break with his first Bundesliga goal of the season.
"It doesn't really change much, he (Wagner) is a player who can play with his back to opponents and secure possession, just like 'Lewy'", said Heynckes.
His teammates Julian Brandt and Kevin Volland are also among the highlighted players for the home side, which sits fourth the German Bundesliga table standings and will move to second place with a win.
Volland pulled one back via a deflection of Niklas Sule in the 70th minute to usher in a period of intense Leverkusen pressure, but Bayern - who introduced new signing Sandro Wagner late on - wrapped things up through James' exquisite stoppage-time free-kick to increase their lead at the top ahead of Schalke's trip to RB Leipzig on Saturday.
Just when the hosts were on the front foot, Bayern doubled the scores out of the blue as Rodriguez passed into the path of Franck Ribery, who had all time and space to place the ball into the bottom near corner in the 59th minute.
Bayern Munich's Robert Lewandowski is set to return. But Martinez pounced to open the scoring for Bayern off the rebound after Sven Bender had blocked Arturo Vidal's header from a corner. Third-placed Dortmund will be hoping to continue their recovery under new coach Peter Stoeger, having won their last two league matches before the break, when they host VfL Wolfsburg on Sunday. However, James Rodríguez sealed the victory with a stunning free-kick in injury time. The 30-year-old Germany striker joined from Hoffenheim.
It was Leverkusen's first defeat at home this season, and ended a 12-game unbeaten run.
"My team played very well tactically over long stretches today, especially in defense", Heynckes said after facing one of his former sides. We are relaxed. The only club that can say no - and would do so - if a player attracted interest is Bayern Munich.