Clon only trailed by 13-10 at half-time but a number of knock-ons robbed them of try-scoring chances.
Conor Kilroy and Declan Coppinger swapped tries in the first half, a Gary Cribb penalty levelled the sides at 13-13 on the hour. However, tries from Eoghan Hickey and Doyle (2) saw the Limerick men through.
Garryowen's great experience told in the end after they had been given a second minute wake-up call when out-half Gary Cribb edged Clonakilty in front with a penalty.
Within two minutes though, Garryowen were in front. Their forwards won a lineout and drove before releasing to scrum half Gerry Hurley. He threw a long pass to Hickey and the other backs were all involved before full-back Kilroy joined the line. He scampered in near the corner for a well-executed try, which Munster's Hickey superbly converted.
Clonakilty suffered a blow when prop Joe Knowles had to retire injured after 21 minutes and his brother Eddie replaced him. Just seconds later, Hickey added a penalty to make it 10-03 for Paul Cunningham's outfit.
But those who expected the sluice gates to open and for Garryowen to take control were badly off the mark.
Clonakilty had not, by any means, gone away and they notched a well-worked try after 25 minutes. It was engineered by their hard-working front eight and after a break by Cribb, Coppinger, their excellent flanker, picked and stormed over under the posts for Cribb to convert and square up the tie.
Hurley then dinked over a neat drop goal to edge Garryowen 13-10 in front at the interval, before a 60th-minute penalty from Cribb levelled again.
But Garryowen struck for three tries in the closing quarter to see off the battling Cork men. A lightning break from Hurley set up Hickey's try. The Garryowen number 9 was halted five metres out but Hickey was on hand to take the pass and waltz over.
With time running out, Clonakilty chose to run the ball inside their own 22 and Doyle swooped on a midfield pass to intercept and race in at the posts to give his side some comfort at 25-13.
The former Ireland Under-21 international added his second try in injury-time when he chased a chip ahead from Hickey, won the race and touched down again.
Scorers: Garryowen: Tries: Conan Doyle 2, Eoghan Hickey, Conor Kilroy; Cons: Hickey 3; Pen: Hickey; Drop: Gerry Hurley.
Clonakilty: Try: Declan Coppinger; Con: Gary Cribb; Pens: Cribb 2