However, the Croatian made amends when he finished off a lovely Sporting move by volleying home Vesga's scooped pass to put Sporting in front after 14 minutes.
At big clubs like Real Madrid, resting several key players together is often considered a taboo and has brought poor results along with it.
Real Madrid will look forward to carry on their march to lift the La Liga trophy in 2017 after a gap of five years, when they face Sporing Gijon away from the Estadio Santiago Bernabeau on Saturday night.
Vesga looped a header over Kiko Casilla to put the hosts back in front after halftime, but Alvaro Morata equalised with a headed goal of his own, before Isco's late victor.
With two-thirds of the B.B.C not exactly firing on all cylinders for Real Madrid in recent weeks, there has been a growing clamor from Madridistas to play their supremely talented playmaker Isco from the start.
Isco scored a last-minute victor as a weakened Real Madrid came from behind twice to beat Sporting Gijon and remain in control of the La Liga title race.
However, even without the likes of Cristiano Ronaldo, Gareth Bale and Karim Benzema, Real for the umpteenth time this season found a late victor to remain on course for a first La Liga title in five years. Zidane said he wasn't sure if Bale would be ready next week to play Bayern in the return leg of the quarterfinal.
One of the only downsides to emerge from their triumph in Bavaria was Gareth Bale being withdrawn in the second half after complaining of a niggle.
And yet Real's reserves gathered enough composure to equalise soon after once again, this time with Morata producing a good header at the far post to penetrate the home outfit's defence for the second time in the match.
On-loan Athletic Bilbao midfielder Mikel Vesga inventively made Sporting's first and put them ahead again with his first LaLiga goal five minutes into the second half.
Madrid then peppered the Sporting goal, but didn't make the breakthrough until the final minute as Isco's effort from the edge of the area had too much power for Cuellar.
Atletico Madrid rested Antoine Griezmann ahead of Tuesday's Champions League match at Leicester, when it will defend a 1-0 first-leg victory.
And with time running out, Isco popped up with another fine finish to hand Real all three points.
Osasuna's Salvatore Sirigu saved two late penalties by Carrasco and Thomas Partey.