Neither of the Silver Arrows' drivers could get the better of Charles Leclerc at Monza, as the Monegasque went on to secure Ferrari's first home win in nine years.
Hamilton's tyres eventually fell off after several laps of intense battle, which saw Leclerc forced into an error and also push the champion wide at the Roggia Chicane and Curva Grande.
Bottas took up the baton after Hamilton ran wide, but made a mistake of his own when he first approached the Ferrari's gearbox and Leclerc raced clear to take his second win in a week.
"It looks like he struggles a little bit when he gets in the wake of the car to extract the maximum," Wolff said of Bottas' lock-up when chasing Leclerc.
"Lewis in that position is able to somehow get closer and put himself in a position to go for a move.
"It's something he [Bottas] has got to work on but on the positive side his racing was great today. He was really fast. Probably in pure race time the fastest car."
Mercedes' lead in the constructors' championship has grown to 154 points following races in Belgium and Italy that Ferrari won, but did not dominate enough to close the gap.
"I think we knew that we didn't have the right package for Spa and Monza," Wolff said.
"Actually second and third was an optimum result for us on the grid, and I said before if we would finish the race in these positions, we'd probably take it.
"As racers now, at the end, obviously there's the feeling of - not entire happiness. You're trying to follow a car, DRS wide open, a long straight, and you're not able to come anywhere close. That is obviously a feeling like not fighting with the right weapons here."
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