But a minor reshuffle merely allowed Mark Butcher to reclaim his old opening slot and get going again after three failures.
Timing the ball completely from the outset, Butcher dominated a 66- run stand with Michael Vaughan until, on 42, he carelessly dabbed a catch behind to gift Rafique his wicket.
Two overs later, Vaughan was run out following a mix-up of playground proportions with Hussain and, thereafter, the former captain scored only a single in 34 deliveries.
Bangladesh lost their best paceman, Mashrafe Mortaza, with a twisted knee seven overs into the innings.
In the first innings, Hussain took nearly six hours and 266 balls for 76 runs. Today, though, the spell was broken from the moment he went down the pitch and hammered Rafique back over his head for four.
Suddenly, instead of hitting shot after shot straight at fielders, Hussain began to find the gaps.
With Graham Thorpe accumulating in his own classy fashion, England made the sort of serene progress expected of them earlier in this series. Rafique, though, is a canny operator and he, at least, gained some satisfaction before the close.
Thorpe, fell leg before wicket on 54 to the spinner as he tried to play across the line. Then, more surprisingly-Hussain's three-hour, 144-ball innings come to its end.
Hussain said: "I don't get out too many times in the 90s so it was a bit disappointing. But the important thing is that the team have had a phenomenal day."
The Essex batsman declared himself "very proud" of his painstaking first innings, which was undeniably valuable in the context of the match.
He insisted: "My timing was fine first time."
England's first star of the day, though, was Johnson. The Somerset man was only on this tour because of Jimmy Anderson's knee injury. He delayed his honeymoon to come on the tour but was not guaranteed a second Test cap until Steve Harmison went home with a back complaint.
But he struck four times during a splendidly hostile and energetic 11-over spell to finish with five for 49. With Saggers picking up two wickets on his debut, England barely missed Rikki Clarke, who could not bowl because he had a f ever, as they dismissed Bangladesh for 152 before lunch.
Having taken six for 33 on debut against Zimbabwe at Chester-le-Street in June, Johnson suffered a knee injury and had to wait five months for another chance.
But there has never been any doubt about his determination and here, given a pitch with a bit of bounce in it, he produced a top notch spell.