Guenzatti was born in Uruguay before moving to the United States at 12. The first team he played for in his new home was the Brooklyn Knights under FA Euro President Joe Balsamo who coaches Sebastian for five years. Together, they won four NY State Cup Championships. Sebastian was Joe's leading goalscorer and starting forward. Sebastian, alongside FA Euro's Marco Balsamo, Adam Marcu, and Ben Marcu went on to represent the United States National Team in the 2002 Danone Nations Cup in France with their long-time coach and mentor, Joe. Sebastian graduated from Francis Lewis High School in Fresh Meadows, New York City. Professional aspirations took Guenzatti back to his homeland, where he played with Peñarol's Under-19 team, before moving to Huracán in 2013.
Guenzatti moved back to the United States on July 5, 2013 when he signed for NASL club New York Cosmos. Guenzatti made his debut for the Cosmos on August 10, 2013 in a 0-0 draw against Tampa Bay. He scored the game-winning goal in the team's 1-0 win over Minnesota United FC on September 14, 2013 and earned NASL Team of the Week honors for his performance. The Uruguayan scored one goal and recorded one assist in ten matches for the Cosmos during the 2013 season and played 86 minutes during the team's 2013 NASL Soccer Bowl championship game 1-0 victory over the Atlanta Silverbacks.
On January 3, 2014, the Cosmos announced that they had signed Guenzatti to a contract extension. During the 2014 Spring season, Guenzatti was tied for second on the team in scoring, recording two goals and two assists in seven matches as the team posted a 6-2-1 (W-L-D) record and finished in second place in the NASL Spring Standings. He earned NASL Team of the Week honors for his Week 7 goal in the team's 1-1 draw with Indy Eleven. He finished the regular season tied for second on the team in scoring with four goals and three assists in 22 appearances (19 starts). He scored the game-winning goal in the team's 1-0 victory over Ottawa Fury FC on July 20, 2014 which earned him NASL Team of the Week honors and he combined with fellow Queens native David Diosa to score in the team's 3-2 win over the Atlanta Silverbacks on September 13, 2014.
In 2015, Guenzatti scored four times in 23 appearances, which included 10 starts. Guenzatti opened the scoring in back-to-back 3-0 wins over the Atlanta Silverbacks (Oct. 7) and FC Edmonton (Oct. 11) He racked up 986 minutes on the field in NASL play. On July 31, 2017, Guenzetti signed with United Soccer League side Tampa Bay Rowdies where is now the team captain and starting Forward.