Simon Easterby, who joined the tour party last weekend as replacement for a stricken Lawrence Dallaglio, moves on to the bench instead of Owen.
It will be Owen's second successive Lions start following his outstanding midweek display against Taranaki in New Plymouth.
The Lions have three games - against Wellington, Otago and Southland - before the June 25 first Test - which underlines Taylor's difficult fight to press his claims.
The 38-times capped forward experienced what the Lions termed as "some discomfort" with his hamstring after training on Friday, forcing him to pull out.
His current situation is depressingly familiar to events on the 2001 Lions' tour, when a knee injury forced him to return home after just one brief substitute's appearance in the opening game against Western Australia.
"Any injury is a concern, but he is getting expert help and hopefully he will be fit for the following week," said Lions coach Andy Robinson after the tourists arrived in Hamilton from their Auckland base.
"It is better to give him more time to recover. We have a big squad and we are able to cope with it."
Speaking before this latest injury blow, Taylor said: "It has been hard. When you are injured, you don't think about anything else apart from how miserable you are."
Taylor's situation will continue to be monitored over the next few days, and although the Lions have plenty of cover in the back-row positions, Owen, for one, will not be available to face Wellington.
He will make a flying visit home on Sunday to be with his pregnant wife, Lucy, before returning to join the tour party.
British & Irish Lions side to play NZ Maori on Saturday June 11 at Waikato Stadium, Hamilton, KO 7.10pm:
15 Josh Lewsey (London Wasps, England)
14 Tom Shanklin (Cardiff Blues, Wales)
13 Brian O'Driscoll (Leinster, Ireland) CAPTAIN
12 Gordon D'Arcy (Leinster, Ireland)
11 Shane Williams (Neath Swansea, Wales)
10 Stephen Jones (Clermont Auvergne, Wales)
9 Matt Dawson (London Wasps, England)
1 Andy Sheridan (Sale Sharks, England)
2 Steve Thompson (Northampton Saints, England)
3 Julian White (Leicester Tigers, England)
4 Simon Shaw (London Wasps, England)
5 Paul O'Connell (Munster, Ireland) VICE CAPTAIN
6 Richard Hill (Saracens, England)
7 Martyn Williams (Cardiff Blues, Wales)
8 Michael Owen (Newport Gwent Dragons, Wales)
16 Shane Byrne (Leinster, Ireland)
17 Gethin Jenkins (Cardiff Blues, Wales)
18 Ben Kay (Leicester Tigers, England)
19 Simon Easterby (Llanelli Scarlets, Ireland)
20 Dwayne Peel (Llanelli Scarlets, Wales)
21 Ronan O'Gara (Munster, Ireland)
22 Shane Horgan (Leinster, Ireland)