The incident comes amid ongoing protests in the occupied West Bank, occupied East Jerusalem and besieged Gaza over US President Donald Trump's recognition of Jerusalem as the capital of Israel.
The Israeli army immediately denied this, saying in a statement "contrary to Palestinian reports earlier today, the (army) did not attack in the northern Gaza Strip".
In October, seven Palestinians were killed after Israeli forces destroyed a tunnel in the strip's southern area.
The two men were reportedly riding through the town of Beit Lahiya on Tuesday when their motorcycle exploded.
Conricus said that Israeli intelligence had monitored the tunnel for months, adding that at no time were any Israeli military personnel or civilians at risk.
Earlier, Israeli planes and tanks shelled positions in Gaza after terrorists fired a rocket toward southern Israel, in what was the latest in a series of cross-border exchanges.
REUTERS Francois Lenoir Mogherini to Netanyahu Israel Should Not Expect EU States to Follow US Decision Jerusalem
"The IDF holds Hamas responsible for these aggressive acts", the spokesman wrote. On Friday, two protesters were shot dead in skirmishes with Israeli troops along Gaza's border.
In recent years Israel has largely refrained from carrying out so-called "targeted killings" of militants in the enclave in an apparent attempt to avoid heightening tensions along the Gaza border.
Since 2008, Israel has launched three offensives on the Gaza Strip.
A third incoming rocket was intercepted by Israel's Iron Dome missile defense battery, the army said.
"The enemy will pay the price for breaking the rules of engagement with the resistance in Gaza", Hamas' Izz ad-Din al-Qassam Brigades said in a statement on Sunday.
On Sunday, Israel said it had destroyed a tunnel dug by Hamas into Israeli territory, apparently for use in an attack.