Connacht won another tight affair between the two sides a fortnight ago to set up this semi-final, and it was more determination that kept up the record of no away side ever winning a Celtic League semi-final, securing a place at BT Murrayfield in the process.
Warriors lost their talisman Finn Russell to injury less than two minutes into the game and Connacht took control of the game when Niyi Adeolokun touched down following a penalty for each side.
An unconverted Leone Nakarawa try got Warriors back into the game in the second half but two more MacGinty penalties, compared to a single Duncan Weir effort, were enough to give Connacht the win in a bruising encounter.
The game was stopped after just 69 seconds as Glasgow Warriors' in-form fly-half Russell went off on a stretcher following a collision with teammate Zander Fagerson, as they tried to tackle Bundee Aki.
Weir came on to replace Russell and Warriors were forced into another change with D'arcy Rae replacing Fagerson at tighthead.
When the game restarted neither side could establish themselves, with the ascendency in possession switching at regular intervals as each team struggled to get a foothold in the opposition's territory.
Warriors were awarded a penalty as the clock approached 20 minutes but Weir turned down a shy at the posts and Fraser Brown's lineout failed to find its target and Connacht escaped with the ball.
Moments later, and following a blistering Aki break, Connacht thought they had scored in the corner through Conor McKeon - however play was called back after the TMO adjudged Aki had knocked on in collecting the ball.
The home side were ahead in the 24th minute, but it was only 3-0 as MacGinty kicked a penalty to give Connacht a lead to represent their growing dominance.
The advantage was cancelled out within two minutes though as Weir bisected the posts after Connacht were penalised for not releasing at the ruck.
The visitors were forced into another change on the half hour mark as Simone Favaro fell victim to a another collision involving Aki and Adam Ashe came on to replace the flanker.
Connacht did get their try in the 37th minute though as Aki placed a kick through the Warriors defence for Adeolokun to skilfully collect and run 30 yards to finish under the posts, MacGinty adding the extras.
The reigning champions almost hit back before half-time but the Connacht defence held Nakarawa up when over their try line, with the referee then blowing for the break.
Half time: Connacht 10 – 3 Glasgow Warriors
Eight minutes after the break Nakarawa did ground it though. The Glasgow battering ram started the break himself with a short lineout and finished the move after darts from Mark Bennett and Stuart Hogg were stopped short of the line.
Weir failed to convert it though, a strong wind blowing the kick off course and meaning Connacht still led by two.
That was stretched back out to five after the 50 minute mark as MacGinty kicked a second penalty, only for Weir to return the favour minutes later as McKeon was penalised for holding on at the breakdown.
With 20 minutes to go Connacht only led by two but the home side were dominant and soon extended their advantage through another MacGinty three-pointer after a period of sustained pressure in the Glasgow half.
Connacht continued to push for the game-winning score and they thought they had it with eight minutes remaining but the TMO denied them again as Adeolokun grounded the ball but MacGinty was penalised for kicking the ball when offside, before it broke wide for Adeolokun to touch down.
When play restarted Warriors were given a lifeline as replacement prop Rodney Ah You was shown a yellow card for a high tackle on Hogg in the Scotsman's own in-goal area.
Try as the champions might to get back into the game, the Connacht defence stood firm and held on to win by five points, setting up a meeting with Leinster at BT Murrayfield for the Guinness PRO12 title.
Full time: Connacht 16 – 11 Glasgow Warriors
Referee: Marius Matrea
Attendance: 7, 800
Man of the Match: Bundee Aki