Bosnian striker Edin Dzeko gave the visitors the lead with a curling shot from the edge of the box in the 34th minute before Trochowski fired in a 25-metre free-kick with the last touch of the match.
Hamburg remain fifth on 35 points from 20 matches while Wolfsburg, still looking for their first win since early November, are 10th.
"For the way we scored the goal we should be happy with the point but for the way we played we should have left as winners tonight," Hamburg coach Bruno Labbadia told reporters.
"We dominated our opponents and had countless chances but we were just too careless."
INTERIM COACH
Wolfsburg, led by interim coach Lorenz-Guenther Koestner after this week's sacking of Armin Veh, went close after five minutes when Brazilian Grafite curled a cross into the box and Dzeko just failed to convert.
Dzeko and Christian Gentner went close again before Hamburg's Markus Berg was denied by keeper Andre Lenz from close range and Mladen Petric sent a 20-metre free-kick against the post.
Striker Dzeko then broke the deadlock when he controlled a deep cross with his chest, turned quickly and floated a left-footed shot past keeper Frank Rost for his ninth league goal of the season.
Hamburg attacked in the second half and hit the woodwork eight minutes after the restart when David Rozehnal headed an Eljero Elia corner against the bar.
Wolfsburg, who have now gone eight matches without victory, must have thought they had won after Hamburg squandered several more opportunities but Trochowski, who came on in the 78th minute, saved the day.
Hamburg's new signing, Dutch striker Ruud van Nistelrooy, watched from the stands.
