The Bulldogs, which captured their first district championship in soccer last week against Notre Dame, also finished their first season over .500 with a 12-11-1 record.
"I really don't know what happened," said Sikeston coach Derrick Long. "We didn't come out like we did against Notre Dame. We weren't the same team. We came out a little flat and they got an early goal on us. We had defensive mistakes on two of their three goals and those are mistakes we haven't made all year."
Affton (15-6-3) advances to the state semifinals where they will take on St. Dominic.
The Bulldogs hung tough the entire match but saw Affton put the game away with four minutes left when Anel Ibrcic scored his second goal of the night.
"We tried to key on him and he got an early goal on us," said Long. "We pretty much shut him down in the second half. He got a late goal when we were pushing everybody up trying to get the equalizer and they got a 3-on-2 situation. Other than that, we did hold him down in the second half. He had some amazing footwork. We tried to double-team him and we had one guy on him, but nothing really seemed to work. We didn't have an answer for the guy."
Ibrcic scored the first goal of the game at the 11:00 mark.
Sikeston sophomore Blake Taylor tied the score at 1-1 when he put one in the net at the 21:00 mark on an assist from Martin Schaefer.
But Sikeston couldn't keep the momentum as Brian Bockius gave Affton the lead right back at the 26:00 mark.
"Taylor's goal was big, but we didn't stay tied long," said Long. "They came back and got one five minutes later. Probably about a minute after that Blake had another chance but he shot it over the goal."
The score remained tied until Ibrcic's second goal at the 76:00 mark.
"We had some opportunities with the ball bouncing around in front of the net and we just couldn't put them in tonight for some reason," said Long.
"They got a late goal with four minutes left and that broke out backs."
Affton out-shot the Bulldogs 21-to-15. Bulldog freshman goalkeeper recorded 18 saves.
"We had a great season," said Long. "Finishing over .500 and beating Notre Dame in that district game -- that was sweet.
It's our best season ever. It's the most complete team we've had here at Sikeston, from the defense all the way up. It's kind of a bittersweet ending tonight, we really wanted to make that final four. On any given night we could've played with this team, but we didn't have it tonight. I feel bad for the seniors. They put it on the line tonight."
Sikeston will lose one of its top goal scorers ever in J.R. Bizzell to graduation and a solid corps on the defensive side of the ball.
But Taylor, and his team-leading 26 goals, along with a strong group of underclassmen return for the team.
"Blake ended up being our leading scorer and with him coming back, Droddy and Carnell, that's a pretty good nucleus," said Long. "Losing J.R. Bizzell is big and three of our defenders. We're going to have to rebuild our defense."