Peter Barker and Alison Waters lost 11-8 11-10 to Australia's David Palmer and Rachael Grinham to give Palmer a first Commonwealth gold.
The 38-year-old then teamed up with Cameron Pilley to win his second title of the day in the men's doubles.
They beat top seeds Nick Matthew and Adrian Grant 10-11 11-7 11-9.
Matthew had been chasing a double after his win over compatriot James Willstrop in the men's singles final.
But former world number one Palmer, who had won two silvers and four bronzes at previous Games, decided to come out of retirement in a bid to win his elusive first title.
Sheffield-born Matthew, 34, and Grant, 33, recovered from a slow start to take the first game, but the Australians took the second to force a decider and held their nerve to force the win.
"In singles there is a planning structure where if something goes wrong it is easier to correct but in doubles there are so many variables and it is such a momentum game," said Matthew.
"We did ourselves proud, we put out game plan into practice but they pulled off two great shots to win."
England's Willstrop and Daryl Selby took bronze after beating Scotland's Alan Clyne and Harry Leitch 11-9 11-7.
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In the mixed doubles, the third-seeded Australians took an early lead but Barker and Waters led 6-2 early in the second before Palmer and Grinham fought back to make it 10-10 and then win the sudden-death point.
"We are disappointed to not convert that lead in the second game," said Barker. "We played well throughout but in the first game they just hit some unbelievable winners.
"It was a great match and I thought we played the best we have all week and we lost to worthy champions."
Palmer and Grinham's team-mates Cameron Pilley and Kasey Brown won bronze thanks to an 8-11 11-9 11-8 success over New Zealand's Joelle King and Martin Knight.

The 21-year-old was taken by "unknown parties" to Aintree University Hospital, Liverpool, in the early hours of Sunday with wounds to his hand and side.
Police said he was stable and the motive for the attack was unknown, although it was thought to be targeted.
They are appealing to witnesses for information.

The 20-year-old has played three times for the Tractor Boys this term, all in the League Cup, scoring one goal.
Yorwerth, a Wales Under-21 international, joined Ipswich this summer after leaving Cardiff City.
He is eligible to make his debut for the Reds, who are currently one place off the bottom in League Two, in Tuesday's visit to Newport County.
Find all the latest football transfers on our dedicated page.
England won silver in both the mixed doubles and men's doubles on the final day of action at the Commonwealth Games squash competition.
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