Build up massive battlefleets to counter his attacks. Make sure you have at least a 5 to 1 advantage, and
focus on defense only.
Then, begin building swarms of stellar manipulation ships - and I mean
swarms. Go to the star systems bordering both your empires and nuke their stars if he's got ships in the system, otherwise make nebulae out of them. You could also do both
Then, send your defensive fleets forward into these (hopefully) shield-negating nebulae and watch his ships die by the masses.
Rinse and repeat until all that's left is his home system, then build masses of construction bases in the systems surrounding it and churn out a massive fleet consisting of both warships and landing ships. Use the warships to take down his defenses,
but do not glass his homeworld! Instead, land lots and lots of troops on it. Then, if there are still other colonies in the system, simply use his own homeworld's massive production capabilities to build a fleet of approx. 100-200 orbital bombers, then glass his planets. If you're feeling really cruel (or you don't need the system at all), pull out all of your ships and nuke the star.
*****
Another approach:
Build massive fleets of ships armed
only with shield depleters, then build swarms of boarding ships. Use the depleter ships to sap his shields, then capture his ships and use his own weapons against him.