The former Red Bull Racing driver, who retired at the end of the 2013 season, said Lewis Hamilton was a bit behind the top two.
Webber described his former team-mate Vettel as better over one lap but Ferrari's Alonso as a 'handful' during an entire race.
"Probably between Seb and Fernando," Webber told the BBC when asked about his toughest opponents in F1.
"You've got to pull everything together. It's hard to say. We've had to always tweak our skill-sets, that last part of our profession – Pirellis, refuelling, one-lap qualifying – all that sort of stuff.
"To try to answer your question, on Sundays Fernando over two hours is a handful. There is no question about that. Over one lap I think he's not with Seb but on Sundays between those two it's very, very tight."
Mercedes' Hamilton falls just behind the top duo, while Webber was unwilling to rank seven-time world champion Michael Schumacher.
The Australian said he never raced against Schumacher at his prime, with one of them always at a stronger team than the other.
"Lewis is handy but probably not quite as much of a machine as those two (Vettel and Alonso) are. They are literally 'plug them in and off they go'. They are very, very handy," Webber said.
"I didn't race Michael really, because he was in a Ferrari and I was in something else and when I was in a Red Bull he was in a Merc, which was further back.
"But those two (Vettel and Alonso) were certainly in their prime when I was."
Mark Webber: Lewis Hamilton has work to do
