Hamilton told BBC Sport ahead of the Abu Dhabi Grand Prix: "Do I put Sebastian in the same category as Fernando? I don't.
"Fernando was my team-mate; I know just how quick he is."
“As a team they are the most deserving and Fernando has done a great job”
Alonso was leading the championship by 40 points from Vettel's team-mate Mark Webber
after the Hungarian Grand Prix
at the end of July, at which point he was the only driver to have won three races this season.
But retirements for the Spaniard at the first corner in Belgium and Japan, and a big upturn in performance from Red Bull have seen Vettel win the last four races, and take three pole positions and four front-row starting spots, to take his victory tally to five for the season.
Alonso has kept himself in title contention all season despite never having the out-and-out fastest car in the dry. His two pole positions came in the wet in Britain and Germany.
Hamilton, who was Alonso's team-mate at McLaren in 2007, said the Ferrari driver had been "incredible" this season.
"Fernando didn't have the quickest car," Hamilton said. "Not a great car at the beginning of the year and he still managed to score some great points. Just massively consistent.
"You know that consistency I was talking about wanting to get? Well, he just toppled mine and kept going and going and going.
Alonso confident on title chances
"He got taken out in Belgium, but the team have just not messed up. As a team they are the most deserving and Fernando has done a great job."
Hamilton also acknowledged Vettel's quality but has emphasised his belief that a lot of his recent performance is down to the car improvements guided by Red Bull's chief technical officer Adrian Newey, F1's pre-eminent aerodynamic designer.
Hamilton said: "Sebastian has been very consistent and the team and Adrian have done an amazing job in this last part of the season."
Alonso said he believes he has driven better this year than at any time in his career, including his title-winning seasons with Renault in 2005-6.
He said: "Last year and this year have perhaps been the best years for me. This is the first time everyone agree for my performance and even when I achieved the world championship not everyone agree. This year's quite amazing for me."
Asked if he believed Red Bull were stronger than Ferrari, he said: "It is not that I think it; it is a fact. They have dominated [these last few races] maybe similar to last year, but in this year we are not 100 points behind, we are 13 points behind."
He added that despite Ferrari's performance deficit, he still believed he could win the championship.
"I truly believe we can win," he said. "Sebastian is on a very good run after four wins, but things have been up and down for everybody and things will change.
"We will get some extra speed, hopefully in this race
[in Abu Dhabi this weekend].
At some stage he will not have a good weekend and we will get our opportunity.
Abu Dhabi Grand Prix 2012, day three
Sunday, 4 November: Race 13:00; BBC One (from 12:10), online and Radio 5 live (from 12:55); Race highlights 19:00 BBC Three.
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