Martin Johnson's side lacked the cutting edge and fluency that marked its record 35-18 win over the Wallabies and went into halftime against Samoa with just a narrow 6-3 lead after blowing a number of try scoring chances.
But the hosts, boosted by a dominant scrum, pulled clear after the break and tries by winger-turned-center Banahan, one of four changes made by Johnson, and replacement flanker Croft saw them home. Flood converted both tries and added four penalties in all to finish with a 16-point haul.
Fullback Paul Williams, who opened the scoring with an early penalty, went over for a try at the start of the second half to put Samoa briefly ahead for the second time but the visitors were hanging on for much of the match.
They scored a consolation try through Fautua Otto as they rallied in the last few minutes.
There weren't the fireworks of last Saturday for England but it clinched two autumn wins in a row for the first time since 2004 - and a sixth successive victory over Samoa - and looks in good shape for the match against South Africa next weekend.
“We ground our way to the win,” Johnson said. “We could have broken them earlier with a couple of tries in the first half that would have changed the game but we didn't.
“It was a very different game to last week, it was very stop-start. Some of the composure wasn't quite there for us but it was still a good experience for the guys.” It was Samoa's second test defeat in a row, coming a week after losing 20-10 to Ireland, but center Seilala Mapusua was delighted with how his team fronted up.
“The team's really come on and there were signs of improvement,” Mapusua said. “We can take a lot of positives out of the game. But England are a quality team and they showed how they can back up wins.” Mindful of keeping the momentum going after the Australia win, Johnson resisted making wholesale changes to his starting team for what was generally perceived to be the easiest of England's autumn matches.
The execution was not quite there this week, however, with Samoa's defense strong throughout a first half England dominated territorially and possession-wise but not on the scoreboard.
“Some of them were a bit quiet in the dressing room (after the game) but I said, 'That's a good win. That's test-match rugby. You don't get it all easy,”' Johnson said. “They've played a tough, physical side today and they will again next week.” Williams kicked Samoa ahead with a fifth-minute penalty but after Ben Foden had a try ruled out for a foot in touch following a wonderful flowing move involving wingers Chris Ashton and Mark Cueto, Flood booted a penalty for 3-3.
England had a second try disallowed when Shontayne Hape's inside pass to Ashton, who blazed through unopposed to the line, was ruled forward by referee Peter Fitzgibbon in the 24th.
Flood kicked a second penalty, in the 26th, and the hosts then camped themselves in Samoa's 22 for the final 15 minutes of the half, winning penalty after penalty in the scrum. But a combination of frantic defending by the tourists and some sloppy handling from England meant the scoreline remained unchanged at the break.
There was time before the interval for flanker James Haskell, one of England's returning four, to be held up over the tryline after a bludgeoning forward effort from lineout ball.
Samoa wasn't in England territory for the majority of the first half but from its first foray after halftime it grabbed its maiden try at Twickenham. From turnover ball, flyhalf Tasesa Lavea fed Williams, who arrowed between Foden and Courtney Lawes to ground on the left for a try the fullback couldn't convert.
England hit back almost immediately as Hape broke free, passed out wide to Ashton, whose inside ball to Banahan allowed the giant center to canter over.
Flood's third penalty of the game put England eight points ahead and after missing in the 59th to blot his copybook, he kicked another for 19-8 in the 71st.
A neat Banahan offload to replacement Danny Care then allowed the scrumhalf to send in Croft for his first international try.
Otto's late score in the right corner, moments after Samoa had won a surprise penalty at scrum time, meant the islanders at least matched England in the try-scoring stakes.
“We weren't as clinical as we wanted to be,” said England captain Nick Easter, who took over the armband in the absence of the rested Lewis Moody. “We got the win but we are not happy with the performance.”
