The Germans moved on to seven points, one behind leaders Manchester United who they host in the next match. Shakhtar are third on five points, four ahead of Real Sociedad.
Leverkusen goalkeeper Bernd Leno was forced into fine saves in the first half as Shakhtar started brightly, eager to take revenge for their 4-0 defeat in Germany, but they failed to break through.
Facundo Ferreyra went close twice but his efforts were well parried by the keeper after trademark low crosses from captain Dario Srna.
Bayer wasted the chance to respond as Sidney Sam sent a weak shot wide from inside the area before Leverkusen were almost caught cold as another Srna cross hit the far post.
The German side forced Shakhtar goalkeeper Andriy Pyatov into a diving save on the hour to parry Son Heung-min's long-range effort.
Shakhtar's Facundo Ferreyra fired over the bar to waste a golden opportunity to put home side in front.
Luiz Adriano nearly stole victory for Shakhtar in stoppage time but his header was well saved.
(Reporting by Igor Nitsak, editing by Ed Osmond)
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