Darren Ambrose's free-kick at the start of the second half had looked to be enough for the Championship outfit, who are 11 places below Wolves in the football pyramid.
Alan Lee had earlier handed the Eagles a dream start after just two minutes when he headed home Ambrose's corner but David Jones ensured the scores were level at the break.
Overall the result was a fair reflection of a stop-start encounter but Neil Warnock will feel he came close to teaching his old apprentice a thing or two, with Wolves boss Mick McCarthy having cleaned his boots during the pair's playing days at Barnsley.
McCarthy made seven changes to his starting XI, suggesting he has one eye on Tuesday's home clash against Liverpool. Wayne Hennessey, George Elokobi, Christophe Berra, Andrew Surman, Sam Vokes, Jones and Zubar all came in from the side that lost 2-0 to Wigan last weekend.
Victor Moses, a January target for several top-flight clubs, was included in Palace's line-up as Warnock made two alterations from the 1-0 win at Plymouth. Alassane N'Diaye and Danny Butterfield came in for Clint Hill and the cup-tied Lee Hills.
A half-full Molineux witnessed an entertaining opening as Vokes tested Palace's Argentinian goalkeeper Julian Speroni inside the first minute, before the visitors silenced the home crowd just 60 seconds later.
Ambrose whipped in a corner from the right and Lee rose unmarked to power a header high into the middle of the net that had too much purchase for Hennessey to keep out.
With Moses and Ambrose pushing forward to turn a 4-5-1 formation into 4-3-3, Palace were proving more than a match for their edgy opponents.
Lee had a chance to grab a second in the 16th minute but he could only fire straight at Hennessey.
There was soon a five-minute break in proceedings, however, as Claude Davis received treatment following a seemingly innocuous aerial challenge with Vokes.
As many as 10 medical staff were joined on the pitch by Eagles boss Warnock before the Palace centre-back was worringly carried off on a stretcher.
When the game restarted there remained a lack of urgency within Wolves' play as they searched for a much-needed spark, although Jones twice tested Speroni from range.
Sylvan Ebanks-Blake wasted a great opening when he opted to shoot well over from 25 yards instead of playing in the unmarked Karl Henry.
But the hosts did pull level in the 37th minute when Kevin Foley floated a cross to the back post after good work from Zubar. The ball was then knocked back by Surman for Jones to finally beat Speroni at the third attempt.
Ambrose whistled a free-kick narrowly wide before referee Chris Foy brought the half to a close.
If Wolves had not paid attention to Ambrose's quality at set-pieces just before the interval then they certainly knew all about it in the 49th minute.
Berra gave away a needless free-kick on the edge of the area for hauling down Lee and the former Newcastle and Charlton man confidently stepped up to accurately curl his effort into the bottom corner.
Wanderers created little as they looked for a way back into the tie, forcing McCarthy to introduce new loan signing Geoffrey Mujangi Bia and Kevin Doyle in a bid to give his side an edge.
And it almost paid off immediately as the latter glanced a header onto the crossbar with his first touch.
Wolves were huffing and puffing as they looked to draw level for a second time, but without seriously threatening.
But their constant pressure was beginning to tell in the closing stages and Berra somehow headed over from two yards when it looked easier to score.
And with 84 minutes on the clock they were finally rewarded.
Wolves recycled the ball on the left and Foley sent another crucial cross to the back post which Zubar chested down, turned and then volleyed a sweet effort past Speroni.
The goal proved to be the last action of the encounter, with both sides set to go again on Tuesday, February 2.