Place jalapeños, skin sides up, on a foil-lined baking sheet; broil 12 minutes or until blackened. Cut peppers in half lengthwise, discarding seeds and membranes. Cut into slices. Set peppers aside.
Place tomato slices on baking sheet; broil 10 minutes, turning after 5 minutes. Place onion slices on baking sheet; broil 14 minutes, turning after 7 minutes.
Bring water to a boil in a medium saucepan. Add peppers, tomato, onion, and salt; return to a boil. Reduce heat; simmer 30 minutes. Cool to room temperature. Mash mixture with hands or with a potato masher. Serve at room temperature or chilled. Store in an airtight container in refrigerator up to two weeks.