Vettel described race-winner Nico Rosberg and teammate Hamilton as like "two buses going for a cruise" over the first few laps as they preserved their tyres in the opening stages, backing up the pack.
After starting from the front row, but given their tyre woes during grands prix this season, it was a tactic that worked for Mercedes.
In response to Vettel's dig, Hamilton said: "He has had the fastest car for the last four years, so it's easy for him to say that. He's got it easy.
"We are making our way up, we are learning, growing, improving with a car that has great potential, so I don't agree with him."
Hamilton has also apologised to Mercedes for his Monaco mistake he is now eager to atone for.
The team were on course for a one-two finish following their qualifying lock-out of the front row.
For the opening 29 laps all was going to plan as Rosberg led Hamilton until an accident involving Felipe Massa brought out the safety car for the first time this season.
It prompted a flurry of pit stops, with the Mercedes duo the last to change tyres and with Hamilton the loser as he dropped from second to fourth behind Red Bull duo Vettel and Mark Webber.
In order to avoid double stacking directly behind Rosberg, the 28 year old slowed and tried to maintain a gap he believed would help, only for it to backfire.
"I wasn't great under the safety car. The double pit stop didn't help and the safety car didn't help," said Hamilton.
"It wasn't the team's fault, it was my mistake. I was told to have a six-second gap and perhaps I had a bit more than six seconds, so I lost out massively.
"I slowed down far too much. When I came round into the pit lane Nico had already done his stop and was gone, so that was really my fault.
"I apologise to the team if I lost them any points because without the safety car I think we could have had a one-two, so [I was] a little unfortunate.
"The win was obviously good for the team. I hope I can contribute points-wise and give them a one-two at some stage.
"I just have to keep working harder because the whole weekend was a missed opportunity."
Lurking in the background, however, is the threat of heavy sanctions from the World Motor Sport Council should the FIA decide to pursue a case against Mercedes for conducting a secret tyre test with Pirelli.
Addressing the issue, Hamilton said: "We were required to do some work, we did some work, it was good fun.
"Right now I'm not concerned about it, that's for the team to worry about.
"I just have to focus on myself and try and get my act together."
Ferrari say suspension the issue in Felipe Massa's crash at Monaco
Ferrari says a suspension failure caused Felipe Massa’s crash at Monaco on Sunday
Ferrari said an examination of Massa’s car confirmed speculation that the crash was caused by an “element of the front-left suspension breaking.”
Ferrari said Massa’s participation at the next race, the Canadian Grand Prix, “has never been in doubt”.
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