The Red Bulls clinched a berth among eight Major League Soccer teams in the final field of 16 teams in the oldest soccer tournament in the United States, dating back to 1914.
The Red Bulls have won all three of their U.S. Open Cup matches and have not used their regular starters in any.
"I'm rather pleased with the performance," Red Bulls head coach Hans Backe said. "We controlled most of the 90 minutes and created a lot of chances. It was a good performance with a clean sheet."
Wolyniec scored his first goal in the 11th minute and add another in the 43rd minute, benefiting from a fine athletic play by rookie midfielder Tony Tchani.
"Tchani has his moments," Backe said. "He's good when he drives the ball like that."
Tchani, the Red Bulls' 2010 first round draft pick carried the ball through three Colorado defenders, then found Wolyniec alone in front of the goal.
Wolyniec has scored two goals in each of the last two U.S. Open Cup matches.
Rookie Conor Chinn added a goal in the 56th minute and Greg Sutton made three saves to collect his second straight U.S. Open shutout.