The incident triggered a rocket siren and the crossing was closed to shipments until further notice.
On Tuesday, Israel opened the crossing to provide Gaza with shipments of gas, food and medicine, but was greeted by mortars shells then as well.
The IDF said that the mortars struck as a convoy of trucks carrying aid donated by international aid organizations was crossing into the coastal enclave. At least one mortar shell hit the Erez Crossing while several others were fired at the Kerem Shalom Crossing on Tuesday.
The incident caused a 19-year-old soldier from the unit overseeing the shipments at the border crossing to be hospitalized with a shrapnel wound to his upper body.
The border was originally closed last Sunday when police arrested 15 stone-throwers near the crossing and planned to re-open for shipments with an IDF unit to oversee the distribution on Tuesday, the border was blocked again after the mortar shells were fired.
The United Nations Relief and Works Agency for Palestinian Refugees in the Near East (UNRWA) demanded that Israel open the border for supplies in a statement on Tuesday.
“UNRWA is urgently awaiting approval through established mechanisms to cross into Gaza,” UNRWA's Director of Strategic Communications, Tamara Alrifai, said in the statement.
However, the Foreign Ministry slammed UNRWA for claiming that Israel is not letting humanitarian aid into Gaza.
"During the transfer of humanitarian aid into Gaza yesterday, via Kerem Shalom crossing, Hamas deliberately bombed the crossing, resulting in the death of two civilians, and over 10 injured, including an IDF soldier," Foreign Ministry Spokesman Lior Haiat tweeted on Wednesday."Today, yet again, Hamas's barrage of mortars halted the transfer of humanitarian aid into Gaza."
Israel will continue trying to transfer aid into Gaza, while taking security into consideration, the Foreign Ministry spokesman said.
Haiat called UNRWA's claim that Israel prevented the transfer of aid "a cynical misrepresentation and simply a lie...The Hamas terrorist organization...is to blame for this situation."
"This is not the first time UNRWA has chosen to twist the facts and misrepresent events, for the sole purpose of blaming Israel. However, yesterday's statement is reaching a new low," he added, calling on UNRWA to change its statement "so it reflects reality."
Lahav Yarkov contributed to this report.