Froome finished eighth, alongside most of the general classification favourites 26 seconds back.
However, the Briton extended his lead by one second to 11 seconds as Esteban Chaves leapt into second following a nightmare stage for Tejay van Garderen.
The American suffered two crashes and a puncture as he lost 17 seconds on the race leaders' group to fall to fourth overall.
A huge early breakaway group of 37 riders was kept in check by the pace set by Froome's Team Sky teammates in the peloton.
Yet, it wasn't until the fifth and final climb up the Puerto del Garbi that the general classification favourites began to fight it out as Alberto Contador attacked and was followed by Froome and Van Garderen.
As Contador and Froome briefly opened up a 15-second gap on their rivals, Van Garderen suffered his first crash of the day.
The chasing group containing Vincenzo Nibali, Fabio Aru and Chaves neutralised that advantage on the descent to the finish line.
Up front Marczynski, Poljanski and Mas were the only three remaining from the breakaway and fought it out in a sprint finish for the stage win.
"I came here very motivated, I thought I could achieve something and today was the day," said Marczynski after the biggest win of his career.
"It was a very tough stage, a big breakaway. We went up the last climb very quickly.
"I said I was going to give it my all and it went perfectly."
The drama wasn't over for Van Garderen as he then suffered a puncture and in his desperation to get back to the peloton hit the ground again upon breaking as he entered a roundabout too quickly.
He did at least minimise the damage to fall just 30 seconds behind Froome overall.
Ireland's Nicholas Roche took advantage of his BMC racing teammate's misfortune to move up to third just 13 seconds back on the four-time Tour de France winner.
Friday's seventh stage contains another three categorised climbs on the 207km from Lliria to Cuenca.