Sanganna polled 60,405 votes as against 47,917 of K Basavaraj Hitnal of Congress with the electoral outcome marking BJP's continuing winning streak in several by-elections held since it came to power more than three years ago.
For Sanganna, who was with JDS before switching loyalties to BJP, it is the fourth victory in the five assembly elections he has so far contested from Koppal.
The ruling party's winning streak in bypolls comes despite being hit by a spate of scams, including illegal mining, which led to the exit of B S Yeddyurappa as Chief Minister after he was indicted by the Lokayukta in its report.
The BJP's victory has come as a booster to Gowda, who became Chief Minister as candidate of the Yeddyurappa group defeating Jagadish Shettar in a secret ballot.
Yeddyurappa had led the BJP campaign in Koppal much against the wishes of his detractors in the party.