Place cloves, allspice, peppercorns, bay leaf, and cinnamon stick in the center of a 6-inch piece double thickness 100% cotton cheesecloth. Bring up edges and tie with clean kitchen string.
In a large saucepan combine undrained tomatoes, onion, vinegar, brown sugar, chipotle, garlic, salt, and spice bundle. Bring to boiling; reduce heat. Simmer, uncovered, for 20 minutes, stirring occasionally.
Remove from heat. Remove and discard spice bundle. Transfer mixture to a blender; cover and blend until smooth. Return all to saucepan. Bring to boiling; reduce heat. Simmer, uncovered, for 40 minutes or until thickened, stirring occasionally (should reduce by half). Adjust seasonings. Cool and transfer to storage containers. Store, covered, in the refrigerator up to 1 month.