Apple surprised Wall Street yet again, but not for the usual reason. This time, the company missed analysts’ estimates for the first time in years, even though it’s selling more iPhones than a year ago.

Shares continued to trade lower this morning after sliding more than 6 percent in after-hours trading yesterday.

At the start of Apple’s conference call with analysts on Tuesday, CEO Tim Cook paid tribute to Steve Jobs, saying the world lost a great leader and mentor; he expressed gratitude for all the condolences.

Cook took over as CEO in August after Jobs said he could no longer meet his duties and expectations in the role. Apple is expected to hold a celebration at its headquarters today for employees to celebrate Jobs’ achievements.

During the quarter that ended Sept. 24, Apple sold 17.07 million iPhone units, which was lower than the 20 million many analysts had expected. It sold 11.12 million iPads during the quarter.

Apple executives said they saw a marked decline in iPhone sales toward the latter part of the quarter, when rumors of the upcoming iPhone 4S release were hitting their stride.

Now, iPhone 4S sales – 4 million in three days – are off to a great start, and Cook said he is confident Apple will set an all-time record for iPhones this December quarter.

Despite competitors, including the Kindle Fire, Cook also said he’s confident in Apple’s existing products and future product pipeline.

Asked about the ultimate objective in ongoing patent disputes, Cook said he didn’t want to comment on any particular litigation but basically, the company spends a lot of time, money and resources on product innovation and “we don’t like it when someone else takes those.”

Apple’s quarterly net profit was $6.62 billion compared with net quarterly profit of $4.31 billion in the year-ago quarter. International sales accounted for 63 percent of the quarter’s revenue.