The incident took place near the Rabin border crossing between both countries.
Israeli Port Authority spokesperson said the injured tourists were from Ecuador.
They are receiving medical attention in hospital, one woman is said to be seriously injured. The gunman, who was on the Jordanian side of the crossing, was shot and killed by security staff.
Israeli border officials said the man passed through the Jordanian border terminal outside the port of Aqaba, crouching among trucks queuing at the Israeli terminal.
Police and port authority officials have sealed off the border crossing and security has been stepped up in the area.
The shootings have marred a day of political talks between Palestinian ministers and armed resistance groups, who are meeting to discuss the possibility of reaching a ceasefire agreement.
Egyptian mediators were to arrive later in the day to take charge of negotiations. They had hoped to kick start the American backed "road map" initiative, which has fallen by the wayside since the US lead invasion of Iraq.
The border crossing is a popular route for tourists travelling to the Israeli resort of Eilat.
Meanwhile, a female Israeli soldier, wounded in w bomb attack on a military base near Tel Aviv has died of her injuries.
Liron Sibony, 19, who was the ninth victim of the 9 September attack at the Tzrifin base, would be buried on Thursday, an army statement said on Wednesday.
The attack at Tzrifin was followed a few hours later by another bombing at a cafe in the German Colony area of Jerusalem.
It brings the overall death toll since the start of the Palestinian intifada in September 2000 to 3,615 including 2,697 Palestinians and 852 Israelis.