Despite being taken the distance, Cleverly always looked comfortable against the mandatory challenger.
The 26-year-old caught Krasniqi hard early on to the delight of the Wembley crowd, but despite the power and accuracy of his shots Cleverly was unable to knock his opponent over.
Krasniqi remained stubborn and in the middle part of the fight he landed some good shots of his own without really hurting the champion.
Cleverly rallied again in the final few rounds, finding some punishing combinations, but couldn't get the stoppage victory he wanted.
The win improves Cleverly's record to 26-0 as he targets a unification showdown later in the year.