"There's something going on in Bordeaux," said home coach Christophe Urios.
Former Fiji international Nemani Nadolo out-did Radradra with a hat-trick of tries as Montpellier eked out a 31-29 home victory over Bayonne.
In Pau, Alivereti Raka, a Fijian-born France winger, scored with three minutes left to give visiting Clermont a 23-21.
French winger Daniel Ikepfan scored two as Toulon won 34-17 at home against Brive to move up to third ahead of Sunday's games.
At a sold-out Stade Chaban-Delmas, the hosts, who have been swapping places with Lyon all season, started the day two points behind. They picked up a bonus point by scoring four tries to one despite falling behind early on.
"Even if we didn't have total control, we didn't panic, we stayed disciplined, we held on," Urios said. "On the whole, Lyon played a better game than us."
Despite losing first place, Lyon remain comfortably ahead of the pursuing pack.
"It was a big test failed," said Jonathan Wisniewski, the Lyon fly-half.
Hooker Mickael Ivaldi gave the visitors the lead after 17 minutes, touching down as the pack shoved over following a lineout. After that Bordeaux-Begles dominated.
The home side replied in the 34th minute. Following a ruck five metres from the Lyon line, the home team moved the ball quickly to the charging Radradra who crashed between two defenders and plunged over.
The Fiji centre had only just returned from a 10-minute break in the sin bin for a high tackle on Lyon fullback Toby Arnold.
Radradra scored again two minutes into the second half.
Bordeaux counter-attacked after a short Lyon kick and ragged chase. Radradra burst on to a pass from Remi Lamerat and into a huge gap in midfield and ran 40 metres to touch down.
Charlie Ngatai and Wisniewski kept Lyon close with two penalties apiece. The visitors trailed by just one point with nine minutes to play but were then sliced open twice.
In the 71st minute, Santiago Cordero broke from the base of a ruck, weaved past a couple of defenders, drew several more and then flipped the ball inside to Seta Tamanivalu who ran untouched to the line.
The Argentina winger then sealed the victory as, once more, a short pass wrong-footed the visiting defence and the centre had an untroubled 20-metre canter to the line.
"We showed that it's not a mistake that we are high up the table," said Maxime Lucu of Bordeaux-Begles.
"We went looking for the bonus point," added Lucu, who came off the bench for last 15 minutes and kicked 10 points. "We kept the ball in hand. We played with a cool head."
"We showed a good face today, but we have to keep it up for another 11 or 12 matches."
In Saturday's late game, Stade Francais' Argentina fly-half Nicolas Sanchez scored an 85th minute try to clinch a 21-20 victory over La Rochelle to move the Parisians out of the relegation zone.
On Sunday, Scotland Six Nations squad exile Finn Russell starts for Racing 92 against champions Toulouse who have South Africa's World Cup winning full-back Cheslin Kolbe playing at outside-half.