After they beat Northern Ireland 3-1 in Rotterdam on Thursday, the Netherlands sit atop Group C.
Germany, the Dutch and the Irish all have 12 points with Northern Ireland having played one game more.
Germany thrashed Estonia 8-0 in Mainz when the sides met last June and German want three more points in Tallinn with the Dutch also away to Belarus on Sunday.
"Our goal is to leave no doubt about it. We have to take three points," said team director Oliver Bierhoff before Saturday's flight east.
Wingers Serge Gnabry and Marco Reus both scored twice in June's rout, but Bierhoff warned against complacency against bottom side Estonia, who have one point from six qualifiers.
"Such games can sometimes be strange. The longer you give teams like that air to breathe, the worse it can get," warned Bierhoff.
Estonia are 86 places below the Germans, according to FIFA rankings, and Bierhoff wants to see evidence of the gulf in class.
"We should make it clear from the first second that there is only one result."
Head coach Joachim Loew had 13 players either injured or ill for Wednesday's 2-2 friendly draw against Argentina in Dortmund, but the situation has eased.
First-choice players Reus, who had a knee knock, plus midfielder Ilkay Gundogan and striker Timo Werner, who both had colds, are now available.
"We want to and will win so that we won't have any problems in the qualification," added Bierhoff.
The Dutch must slip up at least once in their remaining qualifiers if Germany are to finish top of the group.
"That is the problem," said Bierhoff, "so it's important for us to win our next three games," he added with the top two teams going through.
Wins over Estonia, then Belarus in Moenchengladbach on November 16 and three days later against Northern Ireland in Frankfurt will see Germany qualify.
Gnabry, who is in great form after scoring four goals for Bayern Munich at Tottenham 10 days ago and also netted in the draw with Argentina, expects a tough time.
The 24-year-old has scored 10 goals in his first eleven internationals.
"We must not underestimate them, especially when they have their fans behind them," said the former Arsenal winger. "They will play very defensively to make it as hard as possible for us."
Freiburg centre-back Robin Koch, who made his debut on Wednesday as a late replacement, will keep his place as Hertha defender Niklas Stark was sent home after a deep cut to his leg in training.
Germany captain Manuel Neuer will be back in goal after understudy Marc-Andre ter Stegen faced Argentina.
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