The Azzurri's front pairing of Giuseppe Rossi and Antonio Cassano hit it off immediately with the pint-sized forwards scoring in the 21st and 39th minutes respecitvely with similar angled drives to give Italy a cushion at halftime.
Fourth-placed Estonia, who had taken four points off Serbia in their past two games, rarely threatened as an exciting Italy side scored a well-taken third goal after 68 minutes through substitute Giampaolo Pazzini.
Italy's fifth win in their six competitive matches under coach Cesare Prandelli put them on 16 points ahead of second-placed Slovenia and eight points clear of Serbia in third with both those teams having played a game more.
"We kept our concentration and played (all) the football," coach Cesare Prandelli told RAI television.
"We're not there yet but Italy are growing in confidence. We can get even better though by being more daring and keeping the ball on the ground to make better use of our quality players."
The former Fiorentina manager added that it was an important performance by the national team in the wake of the latest match-fixing scandal to beset Italian football.
"We can help (the situation) by showing our commitment and enthusiasm and by transmitting the right values," he said.
CLEVER MOVEMENT
On a cool night in Modena, Italy's diminutive strike duo began the game on fire, pulling the Estonia defence around with their pace and clever movement.
After 14 minutes, Rossi sent Cassano through with an astute pass and only goalkeeper Sergei Pareiko's feet stopped the forward's shot finding the net.
Five minutes later and Cassano returned the compliment only for Rossi to be thwarted by Pareiko's body.
A rampant Italy did make the breakthrough soon after though as Cassano squared the ball to Rossi who, in acres of space, rode two challenges before finding the near corner of the net with a fierce left-foot shot from 12 metres.
Rossi then struck the post with another crisp left-footer before Cassano, picking up a flicked pass from Riccardo Montolivo, shielded the ball inside the box and fired home right-footed in off the far post.
The four-times world champions continued to press in the second half and after Andrea Pirlo struck the post with a low free-kick after 65 minutes, substitute Pazzini grabbed the third, running onto an exquisite chip from Montolivo to sidefoot home.
Without key midfielder Aleksandr Dmitrijev and Konstantin Vassiljev, their top scorer in qualifying, Estonia struggled to get beyond the halfway-line, with late shots from Raio Piiroja and Jarmo Ahjupera failing to trouble Gianluigi Buffon.
