The 23-year-old Edinburgh University student, who came through the ranks at Milngavie & Bearsden ASC, swam the second leg of the final at the Gold Coast.
Thorpe and team-mates Duncan Scott, Kieran McGuckin and Stephen Milne clocked a new national record of 3 minutes 15.86 seconds to finish third in Friday's final.
Hosts Australia were convincing winners with England in second place and the Scots defeating New Zealand and Canada in the race for bronze at the Optus Aquatic Centre.
Thorpe was back in the pool on Saturday for the 100m freestyle individual heats and clocked 49.82 seconds to make it through to the semi-finals.
But despite improving that to 49.75 in his semi that, as 12th fastest, wasn't enough to get him into the final.
Meanwhile there was disappointment for former Balfron High School pupil Ross Murdoch who finished out of the medals in the 100 metres breaststroke.
Murdoch, silver medallist in the 200m earlier in the week, finished fifth as England's Adam Peatty, as expected, took gold.
Milngavie's Calum Tait, who finished seventh in the 200m, just missed out on a place in the final. He made it through the heats into the semi-finals but his semi-final time of 1:01.62 wasn't enough to earn him a place in the top eight and a spot in the final.