The talisman former England back row was taken to hospital with an ankle injury and his departure from the pitch early in the second quarter coincided with a dip in the Lions' fortunes.
Sir Clive Woodward's men made a dream start with two tries from Josh Lewsey and a Mark Cueto touch down helping them to an early 17-0 lead, but Bay of Plenty struck back to level 17-17 at the interval.
The Lions regained control in the last half-hour thanks to Ronan O'Gara's tactical kicking with tries from Tom Shanklin, Dwayne Peel and Gordon D'Arcy giving Woodward his first triumph in New Zealand.
The tourists raced out of the blocks and crossed with just two minutes on the clock. Skipper Brian O'Driscoll made the initial break and then supplied the dummy run on O'Gara's pass which allowed Lewsey to scamper over.
Television match official Paddy O'Brien confirmed Lewsey had claimed his second try after the England star accepted the scoring pass from Wales openside Martyn Williams and dived in at the corner.
Bay of Plenty remained under heavy pressure with Cueto adding a third try in the 11th minute as the Lions sustained their impressive opening, a crossfield kick from O'Gara setting up Cueto beautifully.
Number eight Colin Bourke capitalised on a poor tackle from O'Gara to get the Kiwis off the mark and the Lions' problems deepened in the 21st minute when Dallaglio was stretchered off.
Bay of Plenty were beginning to play with more conviction, finishing one 31st-minute attack with a Murray Williams penalty before the fly-half converted his own try shortly after to level the score.
Winger Shanklin showed strength to finish in the left corner in the 52nd minute, concluding a sustained assault, Williams replied with a penalty and then Peel darted over after a powerful Lions scrum.
The Lions' superior strength and fitness were evident in the last 10 minutes and another try appeared inevitable with a blistering run from Lewsey allowing substitute D'Arcy to complete the scoring.