Sprinkle tomato and onion with pickling salt; let stand 4 to 6 hours. Drain and pat dry with paper towels; set aside.
Combine brown sugar and vinegar in a Dutch oven; cook over medium heat, stirring constantly, until sugar dissolves.
Place mustard seeds and next 3 ingredients on 6-inch square of cheesecloth; tie with string. Add spice bag, tomato, onion, and 3 cups water to vinegar mixture.
Bring to a boil, stirring constantly; reduce heat, and simmer, stirring occasionally, 25 minutes or until tomato and onion are tender. Remove and discard spice bag.
Pour hot mixture into hot jars, filling to 1/2 inch from top. Remove air bubbles; wipe jar rims. Cover at once with metal lids, and screw on bands.
Process in boiling-water bath 10 minutes.