Fontenot was in an 0-for-16 slump before he singled and scored in the sixth. He snapped a two-all tie with a run-scoring single in the seventh after the Cubs blew a 2-to-0 lead the previous inning.
Former National Daryle Ward added two hits and two R-B-Is as the Cubs won for the eleventh time in their last 13 games. They took three of four in the series to pull within four and a-half games of first-place Milwaukee in the N-L Central.
Dmitri Young tripled home a run and scored another for the Nationals, who've dropped eight of ten.
Will Ohman retired two batters in the sixth to move to 1-and-4. Bobby Howry picked up his fourth save with a hitless ninth.
Luis Ayala dipped to 0-and-1.