Although they enjoyed the better of the opening half exchanges they trailed at 5-3 half-time after wing Danny Riordan scored in the left-hand corner with just a minute of normal time remaining. Paul Warwick had kicked them into the lead with a sixth minute penalty and a second effort came back off the upright.
With the wind in their backs Munster regained the lead with a 41 metre Warwick penalty in the 42nd minute and ten minutes later Declan Kidney introduced Frank Sheahan, Marcus Horan, Paul O'Connell and Rua Tipoki and following that the introduction of Ronan O'Gara and Tomas O'Leary raised the tempo of the Munster performance and O'Gara's 61st minute penalty put his side four points clear.
Munster had to survive a number of close-in line outs before Howlett scored his crucial score.
Munster: D Hurley; D Howlett, L Mafi, D Leamy, I Dowling; P Warwick (R O'Gara 58 min), P Stringer (T O'Leary 58 min); T Buckley (M Horan 52 min) (T Buckley), J Flannery (F Sheahan 52 min), J Hayes; D O'Callaghan, D Ryan (P O'Connell 52 min); A Quinlan, D Wallace, A Foley capt (R Tipoki 52 min).
Connacht: G Duffy; M Mostyn, M Deane, K Matthews, D Riordan; A Dunne, C O'Loughlin; B Wilkinson, A Flavin, R Morris; D Gannon, A Farley capt; J Muldoon, J O'Connor, C Rigney. Replacements: J Fogarty, B McGovern, A Browne, L Casserly, C McPhillips, T Nathan, D Yapp.