Brennan Martz, Dustin Krahn, Justin Frey, and Owen Null each had a hit for Cecil, who mustered just seven hits and one run in the tournament.
Cecil went up in the top of the second. With one out, David Jackson reached on an error, Frey walked, and Null singled to load the bases. Jackson scored on a sacrifice fly by Chris Roosevelt.
Schenectady took the lead with two runs in the home half of the third.
Cecil had an outstanding opportunity to tie the game or take the lead in the sixth, but left the bases loaded. The Skipjacks were retired in order in the seventh.
Cecil's starting pitcher, Roosevelt, recorded five strikeouts in five innings of work. Martz fanned two in a perfect inning.