A CT scan this week showed that Jones, who was revealed to have had a fracture in his foot after the 2011 combine, suffered a fracture in the same location. Jones will see Dr. Robert Anderson late Wednesday afternoon in Charlotte, N.C. Anderson did the surgery on Jones' foot in 2011.
Falcons coach Mike Smith addressed Jones' status during a news conference Tuesday afternoon, saying it was "premature" to call it a season-ending injury.
But Smith acknowledged that "the first diagnosis was not encouraging" before confirming that Jones will seek a second opinion Wednesday in Charlotte.
The possibility that Jones could miss the remainder of the season came as a surprise to him, a source close to the Pro Bowl receiver told ESPN. Jones has said that the pain in his foot is not unbearable, according to the source.
Jones will seek the second opinion from noted foot specialist Dr. Robert Anderson, a source told ESPN.
Jones suffered the injury during Monday night's 30-28 loss to the New York Jets. X-rays taken after the game were clean, but Jones had a CT scan Tuesday morning that might have indicated a more serious injury.
"I don't want to get into the specifics about what foot it is," Smith said. "He did injure his foot last night and was able to complete the game. He had a test this morning and is going for a second opinion tomorrow. The first diagnosis was not that encouraging."
Jones has a league-leading 41 catches for 580 yards -- second only to New Orleans' Jimmy Graham -- and two touchdowns this season. The Pro Bowler is second in the NFL with 231 yards after catches.
"He's going to be a hard guy to replace, if we have to replace him," Smith said Tuesday.
The injury is to the same foot that Jones injured before the 2011 season, a source said. The day after his workout at the 2011 NFL combine, Jones was diagnosed with a broken foot and eventually underwent surgery. Despite the injury, Jones was selected by Atlanta with the sixth overall pick and appeared in 13 games that season.
Fox Sports earlier reported that Jones might be out for the year.
Losing Jones would be a significant blow for a Falcons team already hit hard by injuries.
Losing Jones would take away quarterback Matt Ryan's top vertical threat. Jones had eight catches for 99 yards against the Jets, including a 46-yarder.
It remained unclear how Jones was injured. He had been limited in practice throughout the season because of knee problems, and he banged up his leg in a Week 4 loss to the New England Patriots.
Harry Douglas is listed as Jones' backup on Atlanta's depth chart. The Falcons also have Drew Davis and Kevin Cone in the receiving corps but likely will have to add another receiver to the mix. The team is not currently seeking a trade for Cleveland's Josh Gordon or any other receiver, a league source told ESPN's Ed Werder.
Weatherspoon was placed on short-term IR with a foot injury and is eligible to return in Week 11.
The Falcons have a bye this week before returning to action against Tampa Bay on Oct. 20.
ESPN NFL Insider Chris Mortensen contributed to this report.