The Toffees dominated from the off but had to wait until the 40th minute to go ahead via a Mikel Arteta penalty after Jo had been fouled by Andy O'Brien in the box.
The on-loan striker then doubled Everton's advantage four minutes after the restart with a great turn and shot from the edge of the box.
He then got his second of the day with an injury-time penalty after Mark Davies had handled Dan Gosling's cross.
For Brazilian misfit Jo, this was the perfect day after a season of misery. Manchester City's £18million signing has failed to impress at Eastlands, culminating in his deadline day move to Everton.
City boss Mark Hughes may well watch this performance by the gangling striker and blink in disbelief as Everton rounded off a great week which has also seen them knock Liverpool out of the FA Cup.
Everton have now reached the 40-point mark, losing just three of their last 20 games, while this success enabled them to complete a league double over Bolton for the second season in succession.
The reward for teenager Gosling, fresh from his goalscoring heroics in midweek, was only his second appearance in an Everton starting line-up.
The hosts were without Marouane Fellaini and Steven Pienaar, who picked up muscle injuries in Wednesday's fourth round replay - giving Jo his debut.
Bolton made just one change from the side that beat Tottenham last time out, O'Brien coming in for the injured Ricardo Gardner.
DominatedEverton dominated the first half and should have been ahead after just three minutes when Tim Cahill missed from barely two yards out.
Leon Osman put Leighton Baines away down the left, and when the cross arrowed into the box, Cahill arrived at full pace to flick a shot wide of the far post.
From then on Everton moved comfortably forward, creating chances against a Bolton side who were unrecognisable from the side who pride themselves on a battling work ethic.
Bolton were under steady early pressure and only a timely intervention from Sebastien Puygrenier in the six-yard box stopped Jo getting on the end of a Cahill touch.
Gary Cahill deflected a Joleon Lescott hook over the bar from a corner, then Jo hooked over after a Gosling cross reached him in the box.
Fabrice Muamba fired over from 20 yards in the 21st minute and a minute later Jo ran onto a Tim Cahill header and fire wide of Jussi Jaaskelainen's right-hand post.
Everton continued to be wasteful when Arteta's clever pass in the box set up Lescott, but his 12-yard effort fizzed over the angle.
Arteta tried himself, but his effort from the edge of the box was saved by Jaaskelainen.
But after 40 minutes Everton were deservedly in front, after Jo was tripped by O'Brien in the box as he moved past the defender. Arteta coolly fired home the penalty.
Phil Jagielka then saw a header clip the bar from a corner by the influential Arteta, before Osman saw a fierce, low drive deflected wide by Gary Cahill's brave challenge.
Doubled leadFour minutes into the second half Everton doubled their lead when Phil Neville's long punt to the edge of the box was superbly taken down by Jo. The Brazilian turned a hapless Gary Cahill with the move, before firing home.
After just one league goal with City this term, the tall Brazilian had every reason to produce a samba-jig of delight.
Gosling went close with a header before the youngster produced a telling right-wing cross for Jo to test Jaaskelainen with a firm, downward header.
On the hour poor, spiritless Bolton sent on Ebi Smolarek and Chris Basham for Muamba and Puygrenier.
Mark Davies was booked for a foul on Arteta before Gosling tested Jaaskelainen again from the edge of the box.
Bolton produced some life with shots from Ariza Makukula and Matt Taylor, but by now it was a token gesture.
Such was their dominance, Everton were able to take off Tim Cahill with 14 minutes left and send on their other bright young prospect, Jack Rodwell.
Joseph Yobo and Andy van der Meyde took over from Baines and Arteta in the closing minutes, with the visitors introducing Mustapha Riga for Makukula.
Tony Hibbert was booked with two minutes left for a foul on Mark Davies, who was adjudged to have handled a Gosling cross in injury-time.
It enabled Jo to convert a penalty which gave him the perfect end to his day and Everton's week.
1st Half Goals
Shots on Target
Shots off Target