The Team Sky rider came fifth in stage 15's mountain finish in the Sierra Nevada after a triple whammy of climbs, 47 seconds behind Colombian stage victor Miguel Angel Lopez.
Bora-Hansgrohe rider Rafal Majka clinched victory in Stage 14 of the 2017 Vuelta a Espana on Saturday after emerging on top after a fearless last-gasp climb to Sierra de la Pandera.
Froome, once again helped to a strong finish by Team Sky team-mates Wout Poels and Mikel Nieve, finished fifth, with Nibali seventh. I had to win.
Marczynski clinched his second stage win of this edition.
The three-time Vuelta victor, riding in his last race before retirement, launched his attack early with 26.5km remaining in the 129.4km stage 15.
Russian Ilnur Zakarin placed second, 36 seconds behind Lopez, to move up to third in the general classification. "It's incredible. I came in this race with confidence but I never expected something like this".More news: IAEA Reconfirms Iran's Compliance with JCPOA
Miguel Angel Lopez (COL/AST) at 0:27, 3.
"I had confidence in rolling to a tempo stable because I knew that the climb was long".
A late surge by Froome over the final meters of the punishing ride and a final special-category ascent allowed him to increase the gap over Vincenzo Nibali from 55 seconds to 1:01. "We have seen everything at this Vuelta. crashes, attacks". Wilco Kelderman (NED/SUN) 0:31, 7.
Sunday is another gruelling mountain stage with a 129.4km ride from Alcalá la Real to Alto Hoya de la Mora, Sierra Nevada.
Majka ensured he was part of the 10-man breakaway that formed a spearhead roughly midway though the stage, but that bunch had been whittled down to just six or so at the penultimate climb, a category-two mountain about 30 kilometres from the finish.
Race favorite Froome had a mechanical issue with around eight km remaining in the 160.1 km (99 miles) stage from Motril to Antequera Los Dolmones and was forced to change bikes.