Protect your data with a recent backup, preferably Time Machine, before executing any commands on the command line. Carefully read, research, and understand what a command does before pressing the Return key as you do so entirely at your own risk. Be aware that you can render you system inoperable by deleting system files.
If you've deleted the app and the app's icon remains in Launchpad, try refreshing Launchpad with the following command in Terminal. Press the Enter key to execute:
killall Dock
If the app icon still persists, you can remove it from the Launchpad database with the sqlite3 command line interface. Replace APPNAME in the following command with the name of the app whose icon you want to remove. The app name will be the same as that displayed in Launchpad. Enter your admin password when prompted:
sqlite3 $(sudo find /private/var/folders -name com.apple.dock.launchpad)/db/db "DELETE FROM apps WHERE title='APPNAME';" && killall Dock
If you prefer to load the Launchpad database and view the record for the app in question using sqlite3 meta-commands before deleting, start with:
sqlite3 $(sudo find /private/var/folders -name com.apple.dock.launchpad)/db/db
To view the tables in the database use this command following the sqlite> prompt:
.tables
Notice that one of the tables is called apps. To view all the records in this table, use:
SELECT * FROM apps;
To view the record for the app in question, use the following command, substituting the name of the app in question for APPNAME:
SELECT * FROM apps WHERE title='APPNAME';
To delete the record for the app in question, substitute the name of the app for APPNAME:
DELETE FROM apps WHERE title='APPNAME';
You'll receive no confirmation, but you can use the Select command again to verify the deletion as the command will not return a record for the app in question.
Finally, to exit sqlite3:
.exit
To finish up, refresh Launchpad with the following command:
killall Dock

If you prefer a GUI solution (mostly), you can view the Launchpad database in a database management tool such as DB Browser for SQLite. Download DB Browser, install, and open. In terminal, locate the Launchpad database with the following command. Enter your admin password when prompted:
sudo find /private/var/folders -name com.apple.dock.launchpad
The result returned should look similar to the following:
/private/var/folders/8b/fdnjcgqj0730mt2pxjx88rwm0000gn/0/com.apple.dock.launchpa d
Triple-click the result to highlight, Control-click the highlighted text, select Services from the pop-up menu, and then Open from the sub-menu to open in Finder. Drag the database file from the Finder window and drop it onto DB Browser's window.

In DB Browser, click the Browse Data button. Select apps from the Table pop-up list.

Scroll the table to locate the record for the app you want to delete. Click the line number for the record at the far left to highlight the row. Click the Delete Record button to delete the record. To undo the delete of the record, click Revert Changes from the tool bar and click Yes from the dialog that appears. If after deleting the record you are sure about the action, Click Write Changes from the tool bar to permanently delete the record. Quit DB Browser.

Back in Terminal, use the following command to see the change in Launchpad:
killall Dock
Man page KILLALL(1)
Man page SQLITE3(1)
http://sqlitebrowser.org/
http://www.sqlite.org/cli.html
http://www.sqlite.org/index.html