After top scoring with the bat to score 75 runs and help Bangladesh post 246, he returned with the ball to finish with figures of 4-35 as the 35-year-old became the first Bangladesh player to take 300 ODI wickets.
"We have been very good in the last five to seven years at home and unfortunately we lost this series, but we can take a lot from what we've shown in this series," Shakib said.
"I thought we showed a lot of character, we could have easily lost 3-0. We thought we were 20 to 30 runs short but our bowlers talked about stepping up and doing a job for the team and all the bowlers contributed."
England's openers Jason Roy and Phil Salt laid the foundation for the run-chase with a 54-run partnership before the tourists lost three quick wickets.
James Vince, Sam Curran and Jos Buttler also got starts but wickets fell at regular intervals as Shakib dismissed three of the top four batsmen.
Shakib almost capped his performance with a five-wicket haul when he trapped Jofra Archer lbw with his final delivery but the England pacer successfully reviewed the decision before Chris Woakes became the last wicket to fall in the next over.
IDEAL START
Earlier, Bangladesh won the toss and opted to bat but all-rounder Curran gave England an ideal start after dismissing the two openers in his first spell.
But Shakib smashed 75 off 71 deliveries while Mushfiqur Rahim (70) and Najmul Hossain Shanto (53) also notched half-centuries to help Bangladesh post a respectable total.
The hosts' last six batsmen failed to build on the middle order's partnerships, however, as England pacer Archer finished with three wickets while Adil Rashid picked up two.
With England defending their ODI World Cup title in India later this year, captain Buttler said the series in Bangladesh helped them get the measure of wickets in the sub-continent.
"We wanted to play on wickets like this and the two that we played on in Dhaka. It's great preparation for us and great to challenge ourselves in these conditions, which I've said are the conditions we find the hardest," he said.
"I think it will be really valuable for us to reflect on this, what we did well and areas that we can improve. We can take that into our game and improve on this building into the World Cup later in the year."
India hosts the 50-overs World Cup in October and November.
England will next play Bangladesh in three Twenty20 matches starting on Thursday.
