Bottas spun when launching from his pit box during second free practice at the Red Bull Ring, narrowly missing the McLaren mechanics and triggering an angry FIA radio message from team manager Paul James, who labelled the spin as "absolutely ridiculous."
After visiting the stewards, it was revealed Bottas had pulled away in second gear in an experiment to try and make up the time lost to Max Verstappen and Red Bull at last weekend's French Grand Prix.
The stewards decided Bottas' actions were dangerous in nature and subsequently added three places to his grid position as well as two penalty points.
Speaking to Sky Sports F1 ahead of qualifying in Austria, Wolff said: "I think it is pretty harsh to be honest because Valtteri is a driver who never takes.. or does anything risky.
"He launched himself out of there, spun the car and a three-place grid penalty but you need to take it on the chin. It is not great for our race strategy."
Asked if the penalty had changed Mercedes' approach to qualifying, he added: "You can't really change things. We can't ask Lewis [Hamilton] to slow down to give Valtteri a pole.
"Flat out, Valtteri knows he very much needs to be in front to not lose too many places."