While the win was hardly the most convincing of Oranje's impressive run it was enough to ensure they moved five points clear in Group D.
After a frustrating opening half substitute Rafael van der Vaart opened the scoring on 47 minutes before Robin van Persie and substitute Ruben Schaken sealed victory.
With closest rivals Hungary drawing 2-2 with Romania it meant Holland - who have not lost a World Cup qualifier since 2001 - are now in full control of the group.
They had to survive a below-par opening 45 minutes, however, as they struggled to break down a stubborn Estonia rearguard.
Wesley Sneijder was their most threatening presence in the opening exchanges as he flashed a long-range effort over before missing a more presentable opportunity inside the area.
It was otherwise hard work for the hosts and when they did have the ball in the net Van Persie was flagged for offside.
Arjen Robben ghosted in from the left but slid his shot across the face of goal before Sneijder had to be withdrawn with a groin injury.
Van der Vaart replaced him but Holland's fortunes did not initially improve as Robben was shown a yellow card after he opted to put the ball in the net long after the offside flag had been raised.
Estonia could have even grabbed a sucker-punch of a goal as the clock ticked over into injury-time when Konstantin Vassiljev drew a double save out of Kenneth Vermeer.
Vassiljev initially tried to catch the goalkeeper out at his near post and when the ball broke back to him he speared a shot that forced Vermeer into quick action to save to his other side.
Estonia's hopes of ending Holland's long winning run were, however, undone within two minutes of the restart.
Right-back Darryl Janmaat forced the opening when he cut inside and played the ball to Van der Vaart whose quick turn allowed him the time to get off a shot that, while not cleanly hit, had the direction to squeeze past Sergei Pareiko.
The goal galvanised Holland and Van Persie headed straight at Pareiko moments later.
The Manchester United striker was not having his best night in front of goal though and wastefully shot after Janmaat had made another break down the right.
Jonathan De Guzman, whose passing had been sloppy on occasions, then fired over from range after a typical Robben run down the left.
But with the game drifting away from Estonia, Van Persie finally found his range 18 minutes from time to make sure of a Dutch win.
The striker ran onto a lofted pass to side-foot a volley that was too strong for Pareiko.
Holland got further reward for a performance that did not perhaps deserve three goals, when Van Persie's cross reached Schaken to rifle in at the far post in the 84th minute.