Gnabry and Reus scored two goals each as Germany ran riot to seal a third win from three games in Group C.
Underdogs Estonia were helpless against a bright young Germany side who now appear to have left last year's World Cup woes far behind them.
The floodgates opened on ten minutes when Ilkay Gundogan started a slick move which saw Reus fire in the opener.
The goal set the tone for the rest of the first half, as Gundogan and Joshua Kimmich tormented the Estonian back line with devastating through balls.
Gundogan was the orchestrator again when Gnabry doubled the lead, and Germany were 3-0 up after 20 minutes Leon Goretzka flicked in a floating ball from Kimmich.
The fourth goal would have been almost identical to the third had Joonas Tamm not hauled Goretzka to the ground inside the box. As it was, Gundogan smashed in the resulting penalty.
Come the 37th minute, it was Reus' turn again, the Borussia Dortmund star finding the bottom corner with a fizzing free-kick from 20 metres.
Gnabry slotted home his second just after the hour mark, before substitute Timo Werner added a seventh with a dainty finish.
By that point, Leroy Sane was the only German left with a frown on his face, after having two goals unjustly ruled out for offside.
Sane finally got his goal shortly before time, rifling in his side's eighth goal on 88 minutes.
Germany's next qualifier sees them host old rivals the Netherlands in Hamburg on September 6.