Mikel Astarloza of Spain won the 16th stage today, a 99-mile route from the Swiss town of Martigny to Bourg-Saint-Maurice. Contador and Armstrong finished in the main pack behind Astarloza and other breakaway riders.
Armstrong, a seven-time champion, had to catch up to Contador after several attackers burst ahead in the second of two long climbs.
Contador, the 2007 champion, leads Armstrong by 1 minute, 37 seconds. Bradley Wiggins of Britain is third, 1:46 back. The Tour ends Sunday in Paris.