"Apologies to the team but I tried the best I could to recover it and we still got good points for today".
Bottas now sits third in the F1 world drivers' championship but already 30 points off of leader Vettel after three races.
"They did a great job and we have to make improvements".
Mercedes have never had a designated number one driver, and team boss Tito Wolff said the desire was to give both equal opportunity at the start of the race.
Hamilton chased Vettel all the way to the end but was ultimately hampered by a mistake earlier in the race.More news: Celtics nail down top seed in East
"That is the interesting question that we need to analyse at the moment and I don't want to pre-empt what the effect will be, or if there will be a outcome", he added.
"After a winter of massive regulation change, we have been in the hunt for race wins at every weekend and that is the big positive for us". But despite being on fresher tyres, Hamilton could not catch up to the quadruple world champion and the Ferrari driver went on to record his second win of the year and saw himself move at the top of the drivers' championship. The Briton racked up almost 100 laps before setting the best time of the day.
Despite the penalty, Hamilton ended up finishing clear of pole-sitting team-mate Bottas, who struggled throughout the race with oversteer.
Hamilton apologised to Mercedes for damaging his own chances by earning a five-second penalty for deliberately slowing Red Bull's Daniel Ricciardo as they pitted for fresh tyres under a safety vehicle early in the race.
The day proved to be hard for Red Bull Racing.More news: Huge comeback win as Cavs take 3-0 lead
SAINZ PENALIZED: Spanish driver Carlos Sainz received a three-place grid penalty for the next race after stewards ruled that he crashed into Canadian Lance Stroll in the Bahrain race.
With clean air ahead Mr. Vettel built up an unassailable lead and the win put daylight between he and Mr. Hamilton in the title fight: 68 to 61 after 3 rounds.
"I think it's going to be one of the closest ones (championships), if not the closest I've personally ever experienced and I'm looking forward to this fight, not only with Sebastian but the other guys as well who are still gonna be in amongst it".
Near the end of the Bahrain GP, Hamilton had good pace on Vettel, but the gap was just too wide and there was the penalty to consider as well.
He passed the Australian on track then served his penalty in his stop, before passing Bottas in the final stint and ending up 6.6 seconds behind race victor Vettel.More news: Brisbane win a thriller over the Wanderers
Bottas, who joined Mercedes in January as replacement for now-retired world champion Nico Rosberg, is 23 adrift of his teammate.
- UK Snap Election Called to Strengthen May's Mandate for Brexit Talks - Lawmaker
- Cavs rally from 26 down to defeat Pacers
- Paul George Hates Everyone
- United Nations condemns North Korea missile launch after Russia, US spar over words
- Russian Federation vetoes Security Council resolution on alleged chemical attack in Syria
- Prime minister asks for backing for early vote
- Samsung Galaxy S8 pre-orders eclipse S7
- USA says Iran could become another North Korea if left 'unchecked'
- Dade says it's following immigration law
- No one will be fired in United passenger dragging incident