A submerged object damaged the Welsh sailor's Hugo Boss yacht on Saturday, damaging his foil which allowed his nearest pursuers to gain ground.
But he managed to stear his boat at more than 20 knots to maintain hislead on French rivals Sebastien Josse (Edmond de Rothschild) and Armel Le Cléac'h (Banque Populaire VIII).
France's Morgan Lagraviere (Safran) moved fourth ahead of Vincent Riou (PRB), 15 days after the race got underway off the French coast.
Vendee Globe standings at 1800 GMT:
1. Alex Thomson (GBR/Hugo Boss) at 18,852.1 nautical miles from the finish
2. Sébastien Josse (FRA/Edmond de Rothschild) at 87.9 miles from the leader
3. Armel Le Cléac'h (FRA/Banque Populaire VIII) at 96.6
4. Morgan Lagravière (FRA/Safran) at 168.6
5. Vincent Riou (FRA/PRB) at 184.2
6. Paul Meilhat (FRA/SMA) at 233.4
7. Jérémie Beyou (FRA/Maître Coq) at 308.3
8. Yann Eliès (FRA/Quéguiner-Leucémie Espoir) at 784.9
9. Jean-Pierre Dick (FRA/StMichel-Virbac) at 1,083.6
10. Jean Le Cam (FRA/Finistère Mer Vent) at 1,085.7