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The Vulgate Romans 1:1 reads
Paulus servus Christi Iesu vocatus apostolus segregatus in evangelium Dei
Paul, a servant of Christ Jesus, called to be an apostle and set apart for the gospel of God
If I wanted to say "Set apart for God" would that be "Segregatus in Deus"?
Depends on the thing set apart. If you're talking about yourself (assuming you're male), you could say segregatus. If the subject is female, it would be segregata, and if it's an undetermined object, segregatum. Nouns all have gender, though, so if it's referring to e.g. a book, name, or house, it would all be different. Same with whether you're referring to one thing or many.
Doing something for another typically gives the dative case, which for Deus is a simple Deo. More clarification on what's being segregating will yield you the full phrase.
The "in evangelium" here is translating εἰς εὐαγγέλιον; εἰς + acc. can denote purpose in obtaining that object, which works less well in Latin and especially with segregatus.
It seems to me that in Deum doesn't work here. In the phrase in evangelium, the preposition in means 'for' in the sense of 'for the purpose of.' Although evangelium can be a purpose for which a person can be set aside, I'm not sure that Deus by itself is. A glance (a very quick one, I admit) in the dictionary didn't show any analogous use of a sentient or divine being as the object of in when it has this meaning. I'd be more inclined to say segregatus Deo, using a dative.
This is a bit tricky, but I'd settle for [apostolus] pro Deo segregatus, which I would interpret as 'set apart for God['s work]'.
