Lewes boss Steven King praised his side's never-say-die spirit as they went top of division one south with victory at Windsor and Eton.
The Rooks took the lead on 36 minutes when Dwain Clarke was tripped and Junior Kadi converted the penalty.
Lewes were denied a second penalty when the referee ignored appeals after the break for a trip on Marc Whiteman.
The hosts laid siege to the Rooks goal for the last quarter of the game, and their pressure appeared to have earned them a point when Dominique Jean-Zepherin was beaten by Keith Scott's header three minutes from time.
However, in the dying seconds, Kirk Watts released Whiteman, and he hit the winner.
Comments: Our rules
We want our comments to be a lively and valuable part of our community - a place where readers can debate and engage with the most important local issues. The ability to comment on our stories is a privilege, not a right, however, and that privilege may be withdrawn if it is abused or misused.
Please report any comments that break our rules.
Read the rules hereComments are closed on this article