The American opened up a three shot advantage at one point with the help of a birdie-eagle start at Chapultepec Golf Club before a double bogey on the sixth stalled his progress.
World Number One Rory McIlroy was three shots off the lead.
There were fast starts all over the course but when the final group got under way, DeChambeau and Van Rooyen threatened to render them irrelevant.
Van Rooyen played a beautiful chip on the first to set up a birdie but DeChambeau followed him in from 16 feet to stay ahead.
The pair both hit remarkable drives onto the green at the par four second and while Van Rooyen made his eagle from 11 feet to briefly take the lead, DeChambeau followed him in from six to get to 14 under.
Reed made hard work of his pars at the first and second but his tee shot on the third was sublime, setting up a close range birdie to get within three.
Van Rooyen hit a branch with his second on the fifth to slip to 12 under and he was joined there by Reed who holed a birdie putt from the fringe.
DeChambeau was just seven feet from the hole and he made no mistake to stretch his lead to three shots.
His serene progress was brought to a screeching halt on the next, however, as he found water with his third on the par five sixth to surrender a double bogey and move back to the field.
Van Rooyen had an incredible stroke of luck on the seventh as he hit a tree and missed the water by inches but he could not take advantage and a bogey dropped him alongside Thomas at 11 under.
The World Number Four had made a rare bogey after a poor tee shot on the first but got up and down on the second, holed from 16 feet on the third and took advantage of the sixth.
He was soon in a share of second as Reed went left off the tee at the eighth and hit a branch with his second, moving DeChambeau into a two shot lead.
An approach to 12 feet on the tenth then saw Thomas trim the advantage back to one.
McIlroy got up and down at the second and put a tee shot to seven feet on the third before another excellent opening shot on the seventh cancelled out a bogey on the sixth.