Recall: Mass Effect ships are absolute garbage. Their shields are only good for stopping physical projectiles. ST weapons are either energy or plasma, save for the torpedoes. That aside, the only size estimates I could find for the Sovereign was 2km length. The DS-2 is 900 kilometers in diameter, if we're going with a completed DS-2 rather than the DS-1 (which was "only" 160km in diameter). To boot, both have shields which can block both physical projectiles and energy weapons.
Even if it came down to a literal battle of attrition with each combatant grinding down the other, the Death Star would win by virtue of being a fucking artificial moon covered in weapons.
By way of reference, an Imperial-class ISD is 1.6km in length. In other words, the Sovereign is only slightly larger than an ISD and has significantly worse weapons and shield tech, and plenty of ISDs have been destroyed by piddly rebel ships. To boot, ST FTL doesn't rely on anything external to the ship. The Death Star could easily kite the Sovereign, making microjumps in to fire the main laser, jumping away and recharging, then jumping back.
No contest. Put the Sovereign against, say, a Super Star Destroyer and it might be a fair fight. Maybe.
Just kidding, the smallest SSDs are still longer than the Sovereign.
Let's be honest here, Mass Effect tech sucks royally in comparison to just about any other mildly competent SF verse. That's why crossovers with it almost invariably are either curbstomps or small/recovering factions encountering the ME universe at large.