Martin always looked comfortable on the course and set the fastest time at all three splits.
99 seconds quicker
He completed the 54km course in just one hour and six minutes which was over a minute quicker than any other rider. Tom Dumoulin finished in second place with Jan Barta crossing the line in third. The Tour de France leader Vincenzo Nibali came an impressive fourth to cement his position at the top of the general classification.
Martin admitted he raced well and was pleased that his legs managed to stay strong all the way round.
According to Sky Sports, the time trial specialist said: "I'm happy with the performance today. I expected worse legs, but right from the start I had a good feeling.
"Sure, I had tired legs, but I recovered well after the mountains so I could set a good pace from the start to the finish. I never really had a weak point. For me I did a perfect race.”
Nibali on course
Nibali now sits seven minutes and 52 seconds above second placed Jean-Christophe Peraud with only one stage to go. If Nibali doesn't crash on stage 21 he will be crowned the Tour de France winner in Paris.
Peraud had an excellent time trial and managed to move up in the overall standings to second place. Thibaut Pinot will make up the podium on the Champs-Elysees as both Frenchmen saw off the challenge of Alejandro Valverde.
Stage 20 result
1 Tony Martin (Ger) Omega Pharma - Quick-Step, 1:06:21
2 Tom Dumoulin (Ned) Giant-Shimano, +1min 39sec
3 Jan Barta (Cze) NetApp-Endura, +1:47
4 Vincenzo Nibali (Ita) Astana, +1:58
5 Leopold Konig (Cze) NetApp-Endura, +2:01
6 Tejay van Garderen (USA) BMC, +2:08
7 Jean-Christophe Peraud (Fra) Ag2r-La Mondiale, +2:27
8 Sylvain Chavanel (Fra) IAM Cycling, +2:36
9 Markel Irizar (Spa) Trek Factory Racing, +2:39
10 Daniel Oss (Ita) BMC, +2:58
1 Vincenzo Nibali (Ita) Astana, 86:37:52
2 Jean-Christophe Peraud (Fra) Ag2r-La Mondiale, +7:52
3 Thibaut Pinot (Fra) FDJ, +8:24
4 Alejandro Valverde (Spa) Movistar, +9:55
5 Tejay Van Garderen (USA) BMC, +11:44
6 Romain Bardet (Fra) Ag2r-La Mondiale, +11:46
7 Leopold Konig (Cze) NetApp – Endura, +14:41
8 Haimar Zubeldia (Spa) Trek Factory Racing, +18:12
9 Laurens Ten Dam (Ned) Belkin, +18:20
10 Bauke Mollema (Ned) Belkin, +21:24