The result allowed the tiny island nation to leapfrog Tunisia and win the group.
Tunisia only needed a draw in their last Group B match to be among 10 group winners to compete in a final round of playoff matches which would determine Africa's five places at the 2014 World Cup.
But they were two goals down before halftime and were unable to launch a comeback.
"This is a big disappointment, I don't know what happened," Maaloul told the La Presse newspaper.
"This was my last match in charge of the national team. I can only apologise for the disappointment. My players were totally hopeless. There were eight of the 11 who did not take any responsibility."
Maaloul had been in the job for less than a year since taking over from Sami Trabelsi following the country's failure to get past the first round at the African Nations Cup in South Africa in January.