In a large saucepan or heavy-bottomed pot, combine the apples, pears, and water. Bring to a boil over medium-high heat.
Reduce heat to medium-low, cover and simmer for 20–25 minutes, or until the fruit is soft and easily mashable.
Remove the lid and simmer uncovered for 5–10 more minutes to allow some of the excess liquid to evaporate.
Use a potato masher for a chunkier texture, or an immersion blender for a smooth consistency. A blender or food processor may also be used once the sauce has cooled slightly.
Stir in the brown sugar substitute, cinnamon, nutmeg, and lemon juice. Simmer for 5 additional minutes.
Remove from heat and allow to cool to room temperature. Transfer to airtight containers or jars for storage.