Primoz Roglic (LottoNI-Jumbo) soloed away to win stage four and go second in GC behind David De La Cruz (Quick-Step), but there was plenty of carnage on the road to Bilbao.
Contador was at the centre of much of it. As the peloton entered the city, the Spaniard was one of the riders brought down by a crash into a road barrier.
After rejoining the peloton, and with around 20km to go, Contador suffered a mechanical and had to swap bikes with team-mate Julien Bernard.
There was still time for a puncture before the stage was out and Contador, who dropped one minute and 28 seconds, was left cursing his luck.
"If I have got through today, anyone can get through anything," he said.
"There are times when you fall and the only thing to do is get back up. It was a pretty bad fall. I'm still hot. It's going to be a tricky night.
"I've had to change my bike in the climb... and at the end I got a puncture."
Stage four result
1. Primoz Roglic (Slovenia / LottoNL) 4:23:46"
2. Michael Matthews (Australia / Sunweb) +3"
3. Giovanni Visconti (Italy / Bahrain)
4. Michal Kwiatkowski (Poland / Team Sky)
5. Simon Yates (Britain / Orica)
6. Patrick Konrad (Austria / BORA)
7. Rudy Molard (France / FDJ)
8. Diego Ulissi (Italy / UAE Team Emirates)
9. Emanuel Buchmann (Germany / BORA)
10. Alejandro Valverde (Spain / Movistar)
GC after stage four
1. David De La Cruz (Spain / Quick-Step) 16:38:43"
2. Primoz Roglic (Slovenia / LottoNL) ST
3. Michal Kwiatkowski (Poland / Team Sky) +3"
4. Alejandro Valverde (Spain / Movistar)
5. Patrick Konrad (Austria / BORA)
6. Rudy Molard (France / FDJ)
7. George Bennett (New Zealand / LottoNL)
8. Ruben Fernandez (Spain / Movistar)
9. Rigoberto Uran (Colombia / Cannondale)
10. Romain Bardet (France / AG2R)
Read the original article on Eurosport: 'It'll be a tricky night,' says Contador after nightmare day