Leipheimer peddled the 34.4 time trial in a stellar 1:02:45, averaging 33 miles per hour to win his first stage. Australian Cadel Evans rolled in 50 seconds behind Leipheimer, while Russian Vladimir Karpets came in third and Ukrainian Yaroslav Popovych fourth.
Contador finished fifth but that was good enough to keep Evans and Leipheimer at bay and hold onto first place heading into Sunday's 90.5-mile stage, which ends along the Champs Elysees in Paris.
Evans came into the penultimate stage trailing Contador by one minute, 50 seconds but trimmed his deficit to just 23 seconds Saturday, while Leipheimer is 31 seconds back. But they face long odds in overtaking Contador in the 20th stage Sunday.
This year's Tour, the premier cycling competition in the world, received a serious black eye from three recent doping-related expulsions, including Denmark's Michael Rasmussen, who was leading the overall standings before removed from the race by his team Wednesday. Last year's Tour also came under scrutiny after American Floyd Landis' victory was clouded by doping suspicions.