Flanagan's absence was felt by Old Boys, a joint leader of the WestpacTrust Cup one-day competition, when it was beaten by Marist which starting Saturday's sixth round had only one win.
Old Boys missed Flanagan's accurate left-arm medium-pacers at the bowling crease and, adding insult to injury, Flanagan was run out in the incident where his tendon injury was sustained.
Flanagan's absence could also be costly when the two-day championship resumes with Old Boys making a bid to wrest the title off Riccarton.
Marist dedicated the match to the memory of a lower grade player from the club, Morgan Timms, 21, who died suddenly earlier in the week, the senior side wearing black armbands.
Old Boys made 154 after being sent in by Marist at Middleton Park with conditions favouring the bowlers after rain the previous day.
Later Chris O'Connell and Sean McWhirter enjoyed better batting conditions adding 50 for the third wicket, both scoring in the 40s, to lay the platform for Marist's three wicket win. O'Connell's 47 came from 59 balls with five fours and two sixes.
Co-leader also beaten
The only consolation for Old Boys was that it did not lose its share of the competition lead with co-leader St Albans also beaten, pipped by one run by Burnside West-University.
Burnside-West made 163 for nine from its 50 overs with extras making the highest contribution. The best batting came from Matthew Everest and Campbell Ogilvie, who added 43 for the fourth wicket.
Canterbury fast-medium pace bowler Chris Martin was the pick of the bowlers, capturing three wickets for 20, with only 12 of those runs coming from the bat.
The odds were tilting in Burnside-West's favour when St Albans slipped to 96 for six, but James Ward and debutant Daniel Baffsky turned the innings around by adding 44 for the seventh wicket. Both had earlier contributed with the ball, Ward's left-arm spinners yielding just 19 runs, while Baffsky took two wickets.
Once the Ward-Baffsky stand was broken, St Albans wanted 24 from eight overs, but two leg before wicket decisions secured by Mark Coster had the home side fall one short with 11 balls unbowled.
The top of the St Albans batting had been toppled by Kristian Nuttall and Ogilvie, who took seven wickets between them.
Riccarton joins front-runners
Riccarton joined Old Boys and Marist at the top of the table, and has the advantage of already having had a bye, when it beat East Christchurch-Shirley by 43 runs on Hagley 3.
Riccarton reached 154 for eight, its scoring slowing as the innings progressed after the openers had scored 48 from the first 10 overs. Danny Grafton and Andrew Reid added 54 for the sixth wicket, while in the quest to up the run-rate, Riccarton suffered four run-outs.
Former Canterbury pace bowler Michael Owens made an impact with two for 17 from eight overs.
The visitors were tied down by a testing Riccarton attack, left-armer Simon Grant, not a first team regular, showing the way with four for 24 from 9.5 overs and four maidens.
Easy victory for Park
Lancaster Park-Woolston had the day's easiest victory demolishing Old Collegians with 25 overs to spare at Garrick Park.
The Old Collegians' batsmen struggled against the combined side's pace attack in good conditions for the bowlers and laboured to reach 129 from 43.4 overs.
By contrast, the home side swept to victory on the back of Robert Tibbotts's accomplished unbeaten 56 in 72 balls with seven fours. Tibbotts and Mark Stewart shared an unbroken stand of 84 for the third wicket in 64 minutes.
Short scoreboards
Old Collegians 129 off 43.4 overs (T Walton 25, M Hudson 24; J Quinn 3-22, A Timpson 2-13, J Stuart 2-25, C McGillivray 2-34) lost to Lancaster Park-Woolston 131-2 off 25 overs (R Tibbotts 56no, M Stewart 22no) by eight wickets.
Burnside-West University 163-9 (Extras 39, C Ogilvie 35, M Everest 30; C Martin 3-20, D Baffsky 2-30) beat St Albans 162 off 48.1 overs (J Ward 40no, G Howell 23, S Knox 20; K Nuttall 4-26, C Ogilvie 3-41, M Coster 2-6) by one run.
Riccarton 154-8 (G Foulkes 27, D Grafton 27, A Reid 30; M Owens 2-17, D Grocott 2-27) beat East-Shirley 111 off 48.5 overs (Extras 22; S Grant 4-24, G Foulkes 3-26) by 43 runs.
HSOB 154 off 49.2 overs (D Cusack 29, A Robertson 22; S Granger 3-24, S McCloy 2-10, D Willetts 2-36) lost to Marist 155-7 off 45.3 overs (C O'Connell 47, S McWhirter 42) by three wickets.
Points after six rounds (* denotes team having had bye)
Riccarton 8*, HSOB 8, St Albans 8, Lancaster Park-Woolston 6*, East-Shirley 4, Old Collegians 4*, Burnside-West University 4*, Marist 4*, Sydenham 2*.