Rising star Novikov had humbled the factory cars on Friday as he established a 30-second lead amid chaos among the pre-rally favourites.
But on stage four, Novikov's M-Sport Ford picked up tyre damage that would also have repercussions for the car's brakes and suspension.
That cost him several minutes, and meant he tumbled down to 11th by the end of the morning loop.
Volkswagen man Latvala was best-placed to capitalise as he had outpaced Dani Sordo through the morning to move ahead of the Citroen.
Latvala continued to pull clear of Sordo after Novikov's drama, establishing an 18.7-second lead before service.
Thierry Neuville has progressed to third for M-Sport, with his team-mate Nasser Al-Attiyah up to fourth following various issues including a loss of brakes for VW's Andreas Mikkelsen.
Following their Friday problems, Mads Ostberg and Mikko Hirvonen are back up to seventh and eighth. Sebastien Ogier's Rally 2 recovery has so far taken him to 15th.
Robert Kubica is still in the overall points-scoring positions in 10th, as well as holding a lead of nearly two minutes in WRC 2.