Disable Custom App at the Profile level

Disable a Custom App in a Profile:

Quick Tip: Only Users with System Administrator or "Modify All" permissions can modify Profile permissions. 

Classic:

1. Go to Setup | Administer | Manage Users | Profiles.
2. Look for the Profile you want to modify
3. Click Edit
4. Under "Custom App Settings" uncheck the Visible checkbox to disable the App
5. Click Save

Lightning:

1. Click the gear icon then go to Setup | Administration | Users | Profiles
2. Look for the Profile you want to modify
3. Click Edit
4. Under "Custom App Settings" uncheck the Visible checkbox to disable the App 
5. Click Save
 

Disable a Custom App in the App itself:

Classic:

1. Go to Setup | Create | Apps

2. Click Edit on the App where you want to remove the Profile from

3. Under Assign to Profiles, uncheck the Profile

4. Click Save

Lightning:

1. Click the gear icon then go to Setup | Apps | App Manager

2. Click the drop down then click Edit on the App you want to remove the Profile from

3. Select User Profiles under App Settings

4. Under Selected Profiles, click the Profile then click the Remove icon

5. Click Save