He said he was left with a ''numbing, tingling sensation'' on the side of his face following the incident.
The pilot then took the plane back over Port Chalmers and around the coast until the weather cleared, he said.
An Air New Zealand spokeswoman confirmed the flight was hit by lightning on approach to Dunedin. It landed without incident and would be inspected by engineers.
''Lightning strikes are not uncommon and aircraft are designed with this in mind.''
Passengers on Flight NZ688 from Dunedin to Wellington and on Flight NZ478 from Wellington to Auckland were put on other planes while engineers inspected the aircraft.
The lightning was part of a storm system that brought high temperatures and rain to some areas of Otago yesterday, but not enough to make a difference in the driest areas.
The MetService issued a severe thunderstorm watch for Otago at 1.34pm yesterday, but the intense rainfall and large hailstones predicted did not come to much, and the watch was lifted at 7pm.