During a hectic 173-km ride from Tours that ended with Britain's Mark Cavendish crossing the line first, Contador's Saxo-Tinkoff team split the peloton with a brutal acceleration 30 kilometres from the finish that left Froome trapped behind.
By the time Froome reached the finish line, one minute nine seconds had been sliced off his lead, leaving him 2:28 ahead of Dutchman Bauke Mollema and 2:45 clear of Spain's Contador.
Spaniard Alejandro Valverde, who started the day second, trailed in behind the bunch and lost 9:54 after suffering a mechanical problem that cost him any realistic chance of a podium finish in Paris.
"Saxo saw their opportunity today and hats off to them. They were rewarded with over a minute," Froome told a news conference.
Contador, the 2007 and 2009 champion, told reporters: "We saw that some guys were dead so we decided to give it a try."
The move was initiated by Australian Michael Rogers, who left Sky to join Saxo-Tinkoff this season.
"I saw riders on the limit and we had the whole team in front so I said to (Daniele) Bennati should we go and we looked at each other and we just went full gas," Rogers told reporters.
"Today was a special stage, we took the opportunity where it lies."
Irishman Nicolas Roche said: "We turned back and asked Alberto if we could go, he nodded so we screamed at Benna "let's go", Bennati went and we buckled up."
SUDDEN ACCELERATION
The peloton had thinned out after 56km when Cavendish's team, Omega Pharma-Quick Step, used the crosswind and a sudden acceleration to power away in a bid to eliminate some sprint specialists.
German Marcel Kittel, who has won three stages in this year's Tour, was trapped behind and never made it back.
Valverde said he suffered a problem with his wheel with 85 kilometres remaining.
He could not rejoin the peloton despite being helped by his team mates as Mollema's Belkin team joined forces with OPQS to keep the Spaniard at bay.
"It's an unlucky day. We were very careful (near the front) but we really got no luck," said Valverde.
Saxo-Tinkoff sports director Philippe Mauduit refused to join forces with Belkin and OPQS, however, saying the move would have been inappropriate.
"We would not work at the front after Valverde had a mechanical. But once he was two minutes behind...," he told reporters.
Cavendish was hardly challenged in the home straight, easily outsprinting Slovakian Peter Sagan to take his 25th Tour de France stage win after being beaten by Kittel on Thursday.
"The guys were tactically brilliant yesterday and for them to come back today and ride even harder, even sooner shows what a special group of team mates I have," the Isle of Man rider told a news conference.
"I'm incredibly proud."
Saturday's 14th stage takes the peloton from Saint-Pourcain-sur-Sioule to Lyon.
The breakaway specialists will have a good chance of prevailing before Sunday's much-feared stage that finishes at the top of Mont Ventoux.
Saturday's ride could also be a chance to shine for Valverde's team mate Nairo Quintana of Colombia.
Quintana is still in podium contention 5:18 off the pace in eighth place overall.
