Perez - an unused substitute in the Magpies' 2-0 win at Barnsley on Tuesday night - drilled home after just 59 seconds to get United off to a dream start at St. James' Park.
It came after a neat passage of build-up play, initiated by in-form midfielder Jonjo Shelvey.
Shelvey's searching cross-field ball was just kept in by Paul Dummett, and the full-back's inviting cross was flicked on by Yoan Gouffran towards the onrushing Spaniard, whose first-time effort nestled in the far corner.
Shelvey again had a part to play in United's second, feeding Matt Ritchie down the right flank, who squared for Perez to convert from 12 yards.
And, just five minutes later, Perez capped off an impressive display by turning provider for Ritchie, who rifled home in front of a jubilant Gallowgate End.
Newcastle now sit three points clear at the Championship summit, with Brighton & Hove Albion replacing Norwich City in second place.
Perez's opener was his first since United's resounding win at Queens Park Rangers last month, and set the tone for what was a largely comfortable afternoon.
Parity had almost been restored with ten minutes on the clock, however, as a rasping left-footed strike from former Magpie Leon Best ricocheted off the crossbar.
Tom Lawrence's corner dropped for Grant Ward and - despite a suspicion of handball - the midfielder was afforded the chance to tee up Best just inside the area.
By and large, however, United were dominant in the opening 45 minutes.
Gouffran almost doubled their advantage after a quarter-of-an-hour, lifting the ball just over the target from a DeAndre Yedlin cross.
Ritchie then saw a 20-yard strike deflect just wide off the leg of Christophe Berra, as the Magpies looked to rubber-stamp their early authority.
The visitors' only other attempt of note before the break came from defender Adam Webster, who carried the ball from deep before firing off-target from just outside the area.
The home support called for a penalty 35 minutes in, as hotshot Dwight Gayle took a tumble following goalkeeper Bartosz Bialkowski's challenge.
The frontman held his line and gathered Shelvey's delicate ball over the defence, but - after attempting to round the Polish stopper - he saw his protests waved away by referee James Adcock.
The second-half began in low-key fashion, with United a touch sloppy in possession in the final third.
After the hour-mark, however, they turned the screw once more.
Ritchie was the first to go close, guiding another fine cross from Dummett wide of Bialkowski's right-hand post.
Gouffran then found a pocket of space just outside the area, and forced the 'keeper into a smart parry with a powerful right-footed effort.
But, Rafa Benitez's side soon had the breathing space their overall performance deserved.
Ritchie latched onto Shelvey's threaded ball before getting the better of Ipswich substitute Josh Emmanuel, and the Scot's cutback was neatly despatched by Perez.
And, within the blink of an eye, Ritchie himself all but ended the game as a contest.
The former Bournemouth midfielder exchanged passes with Perez deep on the left flank, before finding the far corner with a precise angled effort.
A double-header against Preston North End now follows for Benitez and his side, beginning with Tuesday night's EFL Cup tie at St. James' Park.