In a large pot, combine apples, pears, onions, brown sugar, salt, cinnamon, ginger, allspice, pepper and vinegar. Bring to a boil over medium heat. Reduce heat and boil gently, stirring occasionally, for about 40 minutes or until onions are translucent and mixture is thickened to a jammy consistency.
Ladle hot chutney into hot jars, leaving 1/2 inch headspace. Remove air bubbles and adjust headspace as necessary by adding hot chutney. Wipe rim and place hot lid disc on jar. Screw band down until fingertip-tight.
Place jars in canner and return to boil. Process for 10 minutes. Turn off heat and remove canner lid. Let jars stand in water 5 minutes. Transfer jars to a towel lined surface and let stand for 24 hours.
Check lids and refrigerate any jars that aren't sealed.