Sharks coach Shane Flanagan took the rare step of reading out a list of his grievances with the referees after the match.
"I thought we were brave. I thought both teams played some tough footy," he said.
"We were a bit clunky when we got in there, we turned the ball over once or twice when we got in good field position.
"I thought it was a good game, just disappointed in how the result came about."
But twice the Sharks bombed eight-point leads, and the Cowboys again showed the courage that has defined their season in spite of key injuries.
Cronulla, who have the worst handling efficiency of the year, didn't help themselves with a typically porous 63 per cent completion rate.
Without co-captains Johnathan Thurston and Matt Scott, the visitors refused to roll over when the Sharks threatened to run away in front of the 16,115 crowd.
They took an 8-2 lead at halftime on Chad Townsend's early try, however, went into the sheds down a man after Maloney's sin-binning.
The Sharks five-eighth was ruled to have taken out a chasing Ethan Lowe moments before the break.
Cowboys winger Kyle Feldt reduced the deficit early in the second half, but the Sharks restored their lead when Jack Bird latched onto a Townsend grubber.
Down 14-6 with 17 minutes to go, Jason Taumalolo carried four defenders over in the 63rd minute before Lowe nailed a clutch penalty four minutes from fulltime.
"We were never supposed to win that game," Cowboys coach Paul Green said.
"Even during the game we created some opportunities that we didn't quite ice.
"There's plenty of improvement left in us too, which is good.
"Typical of the year we've had - plenty of guts, plenty of character."
Finals week two:
Broncos v Panthers, Friday, 9.55pm
Eels v Cowboys, Saturday, 9.40pm
Bye - Storm, Roosters
