Super Vegeta is slightly different than Super Saiyan. Super Vegeta 1 and 2 are better for ki attacks and Super Saiyan 1 and 2 are better for physical attacks.
Following the same process as with Super Saiyan, Super Vegeta can be obtained through the PQ 16.
You need to fulfill the quests objectives, and there is a chance that Vegeta will go Super Saiyan. To unlock this quest hidden objectives and make Super Vegeta appear, you have to do something specific, have a look at the quest description. If you defeat him, there is a chance the Super Vegeta skill will drop.