The glitch caused iPad software - used by the planes' pilots and co-pilots for viewing flight plans - to stop working.
The firm's cockpits went "paperless" in 2013 to save its staff having to lug heavy paperwork on board. AA estimated the move would save it more than $1.2m (£793,600) in fuel every year.
The company said that it had now found a fix for the problem.
"We experienced technical issues with an application installed on some pilot iPads," said a spokesman.
"This issue was with the third-party application, not the iPad, and caused some departure delays last night and this morning.
"Our pilots have been able to address the issue by downloading the application again at the gate prior to take-off and, as a back-up, are able to rely on paper charts they can obtain at the airport.
"We apologise for the inconvenience to our customers."
American Airlines pilots use an app called FliteDeck, which is made by the Boeing subsidiary Jeppesen.
A spokesman for the firm provided further detail.
American Airlines said its pilots often carried more than 35lb (16kg) of paperwork
"The issue was caused by a duplicate chart for Reagan National Airport in American's chart database," said Mike Pound.
"The app could not reconcile the duplicate, causing it to shut down.
"We were able to remedy the situation quickly, and instruct pilots to uninstall and reinstall the app.
"Until the chart database is updated, AA pilots flying to or from National will use PDF [portable document format] images of the chart, outside of the app."
Electronic flight bags
Serge Gojkovich, chief executive of car parking app-maker Curbstand, was among the passengers affected.
He tweeted that his San Francisco-to-Los Angeles flight only got airborne on Tuesday after its pilots told passengers they had printed off the maps they needed.
Mr Gojkovich suggested that the pilots of his flight printed out the materials they needed
American Airlines is not the only carrier whose pilots and cabin crew have switched from using physical charts and paper manuals to tablets.
United Airlines was also an early adopter of iPads, while Delta has opted for Microsoft's Surface tablets instead.
British Airways and Ryanair are among others still in the process of shifting to so-called Electronic Flight Bag-based systems.
In addition to saving on fuel costs, it is also suggested that such kit reduces flight preparation time, reduces the likelihood of injuries and helps staff by offering real-time updates.
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