Marcel Kittel o'r Almaen oedd y cyntaf i gyrraedd y llinell derfyn yn Liege, gyda Thomas yn seithfed.
Mewn glaw trwm ac amgylchiadau anodd, cafodd Thomas a phencampwr y llynedd, Chris Froome, hefyd o Team Sky, ddamwain ar hyd y daith, ond llwyddodd Thomas i gyrraedd y terfyn yn ddianaf.
Ond Geraint Thomas sy'n parhau ar frig y tabl ar sail amser.
Dywedodd Geraint Thomas fod y profiad o ddod yn fuddugol yn y ras yn erbyn y cloc ddydd Sadwrn yn anghredadwy, a diolchodd i'w gefnogwyr am eu dymuniadau da.
Bydd y trydydd cymal yn dechrau yn Verviers yng Ngwlad Belg ddydd Llun, ac yn croesi'r ffin i Ffrainc cyn gorffen yn Longwy.
Tabl y Tour de France wedi dau gymal
1. Geraint Thomas (Prydain/Team Sky)     -  4:53:10"
2. Stefan Kueng (Swisdir/BMC Racing)     -  +5 eiliad
3. Marcel Kittel (Yr Almaen/Quick-Step)   -  +6 eiliad
4. Vasil Kiryienka (Belarws/Team Sky)       -   +7 eiliad
5.  Matteo Trentin (Yr Eidal/Quick-Step)   -  +10 eiliad
6.  Chris Froome (Prydain/Team Sky)        -  +12 eiliad
Gallwch wylio uchafbwyntiau'r Tour de France ar S4C yn ddyddiol.

The owner of the 1977 Ford Mustang died in August and when his daughter checked his garage in Welwyn Garden City, she found that the car had disappeared.
The family last recall seeing the car, registration VTM 648S, in 1995.
Hertfordshire Police said: "We have exhausted all lines of inquiry and are waiting for any new information."
It is understood the reason the car's disappearance went unnoticed for two decades is the owner was not well enough to visit the garage it was housed in.
The force said it was convinced the car was not sold by the owner, as his daughter said she would have been informed, and all of the documentation is still in her late father's house.
Police appealed for information about the missing Mustang six months ago but have yet to receive any leads in the case.
Bydd Geraint Thomas yn gwisgo crys melyn y Tour de France unwaith eto ddydd Llun er nad enillodd ail gymal y ras.
[NEXT_CONCEPT]
Police say they have reached the end of the road in their search for a classic car thought to have been stolen during the last 20 years.