The game was short on clear-cut chances but with eight minutes remaining Battocchio fired home from the edge of the area after a shot from fellow replacement Davide Faraoni had been blocked.
Watford made most of the early running and had the first good chance in the 10th minute when Lewis McGugan put Troy Deeney in behind the Latics defence and he laid the ball back for Daniel Pudil, but his side-footed finish was too close to Scott Carson.
Wigan thought they had taken the lead eight minutes later when Manuel Almunia could only push James McClean's low cross from the left-back into the heart of the penalty area and Nick Powell converted the rebound, but the goal was ruled out for a marginal offside decision.
The visitors suffered a blow midway through the opening half when Marc-Antoine Fortune was forced off through injury and was replaced by Callum McManaman but they had a couple of half chances, with Jordi Gomez forcing Almunia into a routine save from a 25-yard free-kick before the former Swansea player then headed a James Perch cross wide.
The early signs had been encouraging but the first half was to become increasingly flat as the contest was played at a relatively subdued pace with both sides lacking intensity.
The Hornets tried to step up the pace at the start of the second half as Fernando Forestieri and McGugan saw shots blocked.
Gianfranco Zola introduced Battocchio and Faraoni to try to add the spark to his side's performance which had largely been absent.
But it was the visitors who had the first decent opportunity of the second period when Powell cut in from the right side of the area and tried a right-footed curler which Almunia parried out to the left side of the penalty area.
McClean turned the rebound back goalwards but Almunia was able to readjust and make the save.
Forestieri had Watford's first on-target attempt of the half soon after with a shot which Carson dealt with comfortably, but Latics boss Owen Coyle was then off his bench when he felt Lloyd Doyley had fouled Powell in the 18-yard box. Referee Andrew Madley was unmoved though.
Zola then dispensed with defensive midfielder Iriney in favour of Diego Fabbrini but it was his two earlier substitutes who were to have the central role in the breakthrough being made.
The goal arrived with eight minutes remaining when play was switched to the right side of the penalty area where Faraoni tried a right-footed shot.
That was blocked but it cannoned across to the edge of the penalty area where Battocchio was not closed down and he took a touch before placing a right-footed finish past the unsighted Carson.
Fabbrini almost added an injury-time second but his powerful strike across goal was tipped away by the Latics keeper.