The 2010 World Cup finalist did not have an easy evening, but three goals after the interval eventually helped the team to victory.
Louis van Gaal's men were unable to break the deadlock before the break, but Rafael van der Vaart gifted Holland the lead only minutes into the second half. Oranje continued to dominate after the opener and Robin van Persie eventually made it two, before Ruben Schaken put the match to bed.
The home side started the match with attacking intentions, yet struggled to create any chances of note early in the game as Estonia defended well. Wesley Sneijder tried his luck from long range twice, but his first attempt went over the crossbar while his second shot lacked power.
Oranje first looked dangerous around the half-hour mark when Daley Blind found Van Persie with a fine cross from the left. The striker then set up Sneijder, who fired wide from inside the area.
An Arjen Robben free kick shortly after almost led to the opener, but Sergei Pareiko was alert and kept the ball out. The Bayern man again threatened minutes later when he dances past two opponents, only to aim just wide from a narrow angle.
Van Persie had by then already seen a goal disallowed for offside, while Robben saw his cheeky lob cancelled for the same reason.
Estonia was initially happy to sit back and defend, yet the team came close to grabbing the lead in the closing minutes of the first half. Sander Puri cut inside from the right before setting up Konstantin Vassiljev in the center of the pitch. The midfielder blasted a powerful shot toward the Dutch goal, which was only just parried by Kenneth Vermeer, who also kept out the rebound.
The Dutch started the second half superbly and needed only two minutes to break the deadlock. Daryl Janmaat charged forward down the right and reached substitute Van der Vaart with a low pass inside the area. The HSV man controlled the ball with his back to goal and turned before beating Pareiko with a low shot.
Van Persie could have doubled Oranje's lead only moments later after a superb cross from Van der Vaart, but his header lacked both power and accuracy. The former Arsenal man again failed to find the net at the hour mark, when his right-footed shot from close range went over the crossbar after some good work from Janmaat.
Nevertheless, the prolific forward got his goal at last in the 72nd minute. Once again Janmaat sent in a dangerous cross from the right, and the unmarked Van Persie volleyed home from five yards out.
Estonia should have pegged one back 10 minutes before the final whistle when Martin Vunk was clean through on goal after a superb pass from Vassiljev. However, the Sillamae Kalev midfielder budged under the pressure and blasted his shot over.
Holland poured even more salt in the wounds in the closing stages of the game. A Van Persie cross fell to Schaken at the far post, and the Feyenoord winger had no trouble finding the net from a narrow angle.
Netherlands remains first in its section with 15 points from five games. The team's next match is at home against Romania on Tuesday.
Estonia sits fifth in Group D with three points from five encounters. It takes on Andorra on March 26.