Four days after featuring in Germany's humiliating 6-0 Nations League defeat to Spain, the £48million man shone against Steve Bruce's Premier League strugglers as Chelsea made it five straight wins in all competitions.
A 10th-minute own goal by Federico Fernandez helped the visitors on their way before Werner's brilliant solo charge in the 68th minute cued up the simplest of opportunities for Tammy Abraham to effectively seal victory.
Sean Longstaff's stunning 30-yard drive which rattled the woodwork proved the only real positive for the home side who simply struggled to match Frank Lampard's confident side for much of the afternoon.
Lampard could have been forgiven for thinking the international break came at the wrong time for his side, who had won four straight games and scored 14 goals in the process prior to the interruption.
His opposite number, however, faced a mini attacking crisis with top scorer Callum Wilson failing a late fitness test and playmaker Miguel Almiron on the bench after a belated arrival back from international duty with Paraguay.
The home side certainly started with intent, Fernandez coming close with a header and Edouard Mendy flapping at a corner, but it did not take long for Lampard's men to establish the kind of dominance that deserved greater reward.
Newcastle keeper Karl Darlow tipped a Werner effort round a post in the fourth minute, then made another fine save to deny Abraham who should have done better after connecting with a Hakim Ziyech cross.
While the manner of the visitors' opener was unfortunate for Fernandez, who stumbled a low cross by Mason Mount and failed to convince the referee of interference by Ben Chilwell, it was also inevitable.
Abraham was inches from connecting with a Werner cross and extending his side's lead in the 15th minute, then Werner himself was equally close to meeting a low cross from the busy Reece James on the right.
Abraham missed another good chance before Newcastle belatedly rallied in the final stages of the first half, Allan Saint-Maximin causing trouble in the visitors' box and hitting a deflected effort high off target.
The half-time loss of captain Jamaal Lascelles to injury hurt Newcastle, and a mistake by his replacement Fabian Schar teed up another chance for Werner, who was put through one-on-one with Darlow but inexplicably sought to square the ball to Ziyech, and Newcastle cleared.
As Chelsea's missed chances began to mount, the hosts began to scent an unlikely opportunity, with Isaac Hayden getting in a dangerous position before being hauled back for handball, and Joelinton curling an effort narrowly wide.
Chelsea responded by doubling their lead in the 65th minute after a scintillating surge by Werner, who burst through the Newcastle back-line before unselfishly squaring to Abraham who slotted home.
Bruce responded by throwing on Almiron in place of Javier Manquillo and Newcastle came close to halving the deficit, Longstaff ramming a shot against the bar from 30 yards, then Andy Carroll finding the side-netting in stoppage time.