Warren had six birdies and a pair of bogeys in his round to go 8-under 208 for the tournament heading into Sunday's final round.
"They were tough conditions on a tough golf course, so to shoot 68 is a very pleasing day," said Warren, who broke 70 for the first time in the tournament.
Ocean winds at Parador de El Saler were stiff, as they often are, but Warren made good use of his short game to move into the lead from two strokes down.
Second-round leader Peter Uijlein was 2-over 74 for the day and fell into a four-way tie for fifth place at 4-under.
Lee finished the day with a 70. He bogeyed the 16th and 17th holes.
David Horsey shot a 66 for the low round of the day and moved into a tie for third place with Paul Waring at 5-under.