Gaza's smuggling tunnels still number in the hundreds despite air attacks and an Egyptian crackdown in which some have been blown up or flooded.
They are a frequent target of Israeli retaliation for attacks by armed Palestinian groups based in the territory.
Smugglers send weapons and goods through tunnels to Gaza to circumvent an Israeli-led blockade.
The attack marks the first Israeli air raid against the tunnels since August 10.
An Israeli military spokeswoman said jets attacked the tunnel after mortar shells were fired from Gaza into southern Israel on Monday, slightly wounding one soldier.
The mortar fire was in turn a response to an incident in which a Palestinian was killed and another wounded by Israeli fire when they approached the border fence with Israel on the northern edge of the Gaza Strip earlier that day.
The border between Gaza, governed by Hamas, and Israel has been largely quiet since January 18 ceasefires from both sides ended a 22-day Israeli war on the Palestinian territory.
The ceasefires have largely held despite violations by Hamas and Israel.