Napoli draw away to Genk in early kick-offs
Barca host Inter later with Lionel Messi starting just his second match of the season as both sides look to join Dortmund on four points following the Bundesliga side's hard-fought victory in the Czech Republic gained thanks to Hakimi's strikes in either half.
The Morocco international burst through onto Julian Brandt's pass in the 35th minute and charged towards the goal, skipping past Petr Sevcik and goalkeeper Ondrej Kolar before rifling home the opener.
The pair combined again in the final minute with another rapid counter, the Germany midfielder this time slipping Hakimi in down the left and the 20-year-old -- on loan from Real Madrid -- slotting a neat left-foot finish that made sure of the win.
"Hakimi sat on his motorbike and raced away from everybody," said Slavia defender Ondrej Kudela.
"Those counter-attacks were lethal, but we made mistakes we cannot make at this level. We had our chances, but wasted them."
Dortmund, who came into the game on the back of three straight draws in all competitions and a lowly eighth place in the Bundesliga, had to ride their luck before Hakimi sealed the points.
Lukas Masopust had already fluffed a one-on-one with Roman Burki in the first half when Stanislav Tecl missed a golden opportunity to equalise when clean through seven minutes after the break, slapping his shot into the side netting with the goal at his mercy.
Sevcik then nearly made up for his earlier shoddy defending with a powerful shot that fizzed just wide with 19 minutes remaining.
Meanwhile in Group E Napoli slipped up with a goalless draw at Genk which came after the Serie A side struck the woodwork three times and striker Arkadiusz Milik missed several chances to win the match.
Carlo Ancelotti's side could have been ahead as early as the 15th minute when Jose Callejon struck the post before Milik then clipped the bar on the rebound.
Off-form Milik then hit the bar again with a header 10 minutes later and Callejon missed a glaring opportunity just before the hour mark when he uncharacteristically shot wide from close range when found at the far post.
They were almost made to pay for their profligacy when Ianis Hagi -- son of former Barcelona and Romania attacker Gheorghe -- blazed over when presented with a golden opportunity to snatch all three points.
"We knew this game could be tough. We should have simply been more clinical, that's all I have to say about the team's performance," said Ancelotti.
Napoli stay top of the group on four points with defending champions Liverpool facing Salzburg later Wednesday.