His Leicester City team recovered from an very bad start, levelling through Jamie Vardy in the second half, but they paid a heavy price when Andre Gray punished some slack defending in stoppage time.
Harvey Barnes wasted an opening and the half ended without Leicester having a shot on target, Wilfred Ndidi finally giving Ben Foster a comfortable save to make in the 51st minute.
What does it mean?
Recently arriving after a stint with Celtic FC, Rodgers' tenure with Leicester has not started off well as he tasted defeat but the former Liverpool boss seems to be focused on doing work as he eyes to sign Youri Tielemans on a permanent deal.
Watford's Andre Gray scored a stoppage-time victor as Leicester City began life under new boss Brendan Rodgers in underwhelming fashion, suffering a 2-1 defeat at his former club in the Premier League on Sunday. I want to leave at the right moment and in my opinion the right moment would be pre-season'. "The key is just coming in and assessing where I'm at with the players".
Leicester looked the likelier side to go on and win the game after Vardy's 10th Premier League goal of the season drew the Foxes level.
"I will always be grateful for Watford, I have said many times".
But Rodgers could not hide his frustration on the touchline when Schmeichel sloppily gave the ball away to allow Deeney and Gray to link up for the victor.
"What we want to do is keep the season alive, that is the most important thing".