The midfielder, who came on for the second half at Holker Street, found the top corner with a 30-yard shot in the 83rd minute to settle Town’s penultimate pre-season match.
Having also scored the equaliser in the 1-1 draw at Stoke City on Saturday, Batty capitalised on good work by fellow substitute Ellis Harrison for the only goal in Cumbria.
The League Two club had begun brightly, wideman Jordan Stevens twice testing Town keeper Jay Lynch early on.
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Fleetwood's first chance of note came on 32 minutes, when Chris Conn-Clarke beat his man on the right and lobbed keeper Paul Farman only to see his effort clear the crossbar.
Conn-Clarke then went closer, forcing Farman into a save, as the first half ended goalless.
The hosts had to play out the last half-hour a man short after having Josh Gordon sent off for a reckless challenge on Dylan Boyle.
Town struggled to take advantage of their extra man as regular breaks for drinks and substitutions meant the game lacked flow.
That was until Batty's strike settled the issue after an excellent Ellis run.
Town went close to a second in the closing seconds but a full-stretch Max McMillan couldn't get on the end of Josh Earl's low cross from the left.
Fleetwood head coach Scott Brown told the club website: “It was a great 90 minutes for us. When your opponents lose a player, that’s when there has to be more intent in your play, making them make mistakes and winning the ball high up the park. But we but we didn’t do that well until Batty’s goal.”
As for the spectacular winner, Brown admitted he hadn't wanted the scorer to shoot.
“I have to say Batty scored a great goal but I was asking for him to pass it and keep the ball,” he said. “But sometimes you have to let the forward players flourish and that’s what has done.”
Fleetwood complete their friendly programme at home to Dundee United on Saturday.
Fleetwood: Lynch, Johnston, Nsiala (Baker 63), Earl, Andrew (Bird 70), Vela (Wiredu 46), Boyle (White 66), Baggley (Batty 46), Hayes (McMillan 70), J.Garner (Harrison 63), Conn-Clarke (Lane 46); Sub not used: Donaghy.