The forward headed Leverkusen ahead on 22 minutes and Simon Rolfes added a penalty early in the second half, his third goal in as many matches in the group stage, after Kiessling had been fouled.
Sidney Sam, top scorer in the Bundesliga this season, added a third and Kiessling pounced from close range as dominant Leverkusen leapfrogged the Ukraine side into second place in Group A on six points, one behind Manchester United.
Kiessling made headlines on Friday when he scored a "phantom goal" against Hoffenheim in the Bundesliga, his second-half header allowed to stand after everyone missed that it had gone in through the side netting.
Leverkusen won the match 2-1 but later said they were embarrassed by the incident which reignited a long debate about whether goal-line technology should be used in Germany and whether a replay should be staged.
There was no controversy, however, as the Bundesliga, who have made their best ever start to a league season, brushed aside a Shakhtar side who offered little attacking threat.
Kiessling rose high to meet Giulio Donati's cross from the right and the ball crept into the left corner past a flailing Andriy Pyatov to put the Germans ahead.
Shakhtar's best moment came just before halftime when Alex Teixeira could only fire into the side netting after a quick counter-attack.
A push in the back on Kiessling by Shakhtar captain Darijo Srna allowed Rolfes to confidently score from the spot and Sam made it 3-0 on 57 minutes with a clinical finish after a pass from Son Heung-Min.
Kiessling, overlooked by Germany for the last three years despite a glut of goals, put the gloss on an easy victory, walking the ball into the net after Pyatov had spilled a shot 18 minutes from time.