Pollard was carted off in the closing stages of the second quarter with a low-scoring game tied at 6-6 at Levi's Stadium.
The running back did not return, and the 49ers claimed a 19-12 win as the Cowboys looked lost on offense in the second half.
Initial reports detailed a high ankle sprain for Pollard, but it has since emerged he also sustained a fracture to his left fibula that will require surgery.
Pollard would therefore have been unavailable for the NFC Championship Game against the Philadelphia Eagles even if the Cowboys had scraped through.
That never appeared likely without Pollard on the field at the end of a career year, however.
The 25-year-old finished the regular season with 1,007 rushing yards, the most on a Dallas team who ran on 45 per cent of plays – the seventh-highest rate in the NFL.
Pollard had nine rushing touchdowns and added a further three receiving scores from 39 catches for 371 yards.
Elliott, who had a comparatively difficult season, could not carry the load in Pollard's absence in San Francisco, finishing with the same number of yards from scrimmage (33) as the injured star despite playing the full game.
Quarterback Dak Prescott acknowledged afterwards Pollard's injury "hurt us", but the first-time Pro Bowler must now hope the serious nature of the problem is not the source of more hurt.
Pollard will become an unrestricted free agent in March, at which point he will still be rehabilitating his left leg.