The Bundesliga club took the lead early on through Jan Rosenthal, but Mario Melchiot equalised shortly after in a frenetic opening period.
Martinez, who saw his side lose to Crewe last week in his first match in charge since leaving Swansea, was therefore forced to settle for a share of the spoils.
It took only eight minutes for Hannover to take the lead in the Austrian Alps as midfielder Rosenthal fired a low effort past Chris Kirkland from the edge of the box.
Wigan, though, responded almost immediately as Melchiot restored parity in the 11th minute when heading in a Charles N'Zogbia corner.
Jason Koumas, who entered the game among a host of half-time substitutions, went close to winning the match for the Latics with a skilful effort.
However, Hannover also threatened in the second 45 minutes and substitute goalkeeper Mike Pollitt was required to be at his best on three occasions.