For the very first time in this series Pakistan batting clicked in first innings of last test and there bowlers did a good job to restrict Aussies to 299. Now in second innings Pakistan should have scored 250 if they can't make another 300. The whole batting line up collapsed on just 115 runs. Pakistan should take some serious actions against its so called best bowlers who either abstained from participating in this series or got unfit in the series.
You are right the innings of Pakistan was far better than the second innings. They lost because of poor batting otherwise they could have either draw the match if they had good lead. Pakistan bowling has not been as it was earlier. I am not sure taking action against the bowler will be the right thing to do who opted out of the test series.
Pakistan's batting performance was so poor that both the innings suffered a massive batting disaster at the start. Especially in the second innings too, the first wicket fell for zero runs and the second wicket fell for one run. The fall of three wickets in a row for 67 runs goes without saying how badly it affects a Test match. The fall of two consecutive wickets for 109 runs was largely due to Pakistan's batting disaster. However, even if the bowling is relatively good, if the batting disaster cannot be overcome, then nothing but defeat in Tests can be expected.