The Reds only had one recognised centre-back available in Bjorn Hardley and struggled to handle the former West Ham forward as the Red Imps took control of proceedings.
Charlie McNeill and Hardley pulled goals back during a stirring fightback as United carried more and more of a threat the longer the tie wore on, although Hannibal was sent off in injury time.
The boys will now need to pick up positive results against fellow Group F sides Sunderland and Bradford City in order to progress as one of the two qualifiers for the knockout stages, although the comeback does aid the goal difference.