Much had been expected of the dual between the German and eventual winner, Fabian Cancellara (RadioShack-Nissan) in the build up to the 6.4km race against the clock, but it was the time of Martin's teammate Sylvain Chavanel which restored some pride for the high-flying Belgian squad.
Martin looked to be on course for the yellow jersey when a flat tire saw him dramatically back off the pace.
"I had a flat tire after the first split time," Martin said. "I could feel that I was slipping away on the last roundabout and thought 'OK, maybe it's just a little bit slippery,' but then I realized I had a flat in the back and had to change the bike. I think it was a quick change, but it kills the morale and the rhythm. I'm really disappointed.
"I still have a good time, and I think would have a made a really good time without the flat tire," he continued. "I wanted to fight for the yellow. I'm disappointed, but I thought 'just keep on fighting, the long time trials are coming.' I can tell I have very good condition and now I have to fight now for the next time trial."
Despite the misfortune, Martin still posted a time that would fall 23 seconds off the winning pace of Cancellara.
French chrono champion Chavanel, celebrating his 33rd birthday, was 113th rider out of the start gate in Liege with over an hour to wait to see if his time of 0:07:20 would stand up to the traditional time trial powerhouses.
"I did a great race," Chavanel said. "I wanted to make a good performance. From the beginning of the season I'm doing good in the time trials. I knew that the specialists could have beat me, but I'm super happy in any case. I have no regrets. I really did my best to honour my brand new French champion jersey. It's a third place in a prologue of the tour against the best time trialists of the world.
"I'm disappointed for the flat tire of Tony," he explained. "Today he was really strong and he could have fought with Cancellara until the end. The Tour is just getting started. I have time to try to attack and do something good. Today is my birthday and even without a victory, we are going to celebrate!"
Chavanel's time endured, and was matched by Bradley Wiggins (Sky) and usurped by Cancellara.
Martin will get another chance for a showdown with Cancellara on Stage 9 with a 41.5km time trial between Arc-et-Senans and Besançon.